Mercurial > repos > iuc > pygenometracks
annotate pyGenomeTracks.xml @ 7:326a3db8d9d1 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
| author | iuc |
|---|---|
| date | Fri, 17 Apr 2020 11:57:44 -0400 |
| parents | 5cec5fb749f0 |
| children | 4ac4e7083b7e |
| rev | line source |
|---|---|
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
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changeset
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1 <tool id="pygenomeTracks" name="@BINARY@" version="@WRAPPER_VERSION@"> |
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0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
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2 <description>plot genomic data tracks</description> |
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2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
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3 <macros> |
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2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
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4 <token name="@BINARY@">pyGenomeTracks</token> |
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2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
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5 <import>macros.xml</import> |
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2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
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6 </macros> |
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2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
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7 <expand macro="requirements" /> |
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2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
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8 <command detect_errors="exit_code"> |
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2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
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9 <![CDATA[ |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
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10 ## First symlink data of hic or bed/gtf to have the good extension |
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c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
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11 #for $counter, $track in enumerate($tracks): |
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c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
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changeset
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12 #if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option": |
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c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
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13 #for $counter_matrix, $data_matrix in enumerate($track.track_file_style_conditional.matrix_h5_cooler_multiple): |
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c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
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changeset
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14 #set ext = $data_matrix.extension |
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c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
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changeset
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15 ln -s $data_matrix ${counter}_${counter_matrix}.$ext && |
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c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
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changeset
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16 #end for |
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c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
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17 #end if |
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c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
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18 #if $track.track_file_style_conditional.track_file_style_selector == "gene_track_option": |
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c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
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19 #for $counter_bed, $data_bed in enumerate($track.track_file_style_conditional.track_input_bed): |
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c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
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changeset
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20 #set ext = $data_bed.extension |
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c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
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21 ln -s $data_bed ${counter}_${counter_bed}.$ext && |
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c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
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changeset
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22 #end for |
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c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
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changeset
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23 #end if |
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c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
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changeset
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24 #end for |
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c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
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25 |
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0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
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26 |
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2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
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27 sed '/^$/d' '$tracks_config' && |
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2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
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28 @BINARY@ |
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2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
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29 --tracks '$tracks_config' |
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2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
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30 #if $region and $region is not None: |
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2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
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31 --region '$region' |
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2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
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32 #end if |
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326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
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33 #if $global_args.title is not None: |
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326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
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34 --title '$global_args.title' |
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326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
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35 #end if |
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326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
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36 --fontSize $global_args.fontsize |
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326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
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37 --dpi $global_args.dpi |
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326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
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38 --trackLabelFraction $global_args.trackLabelFraction |
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326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
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39 --trackLabelHAlign $global_args.trackLabelHAlign |
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0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
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40 --outFileName plot.$image_file_format |
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2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
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41 && mv plot.$image_file_format plot |
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2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
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42 ]]> |
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2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
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43 </command> |
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2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
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44 <configfiles> |
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2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
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45 <configfile name="tracks_config"> |
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326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
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46 ## Each track: |
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2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
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47 #for $counter, $track in enumerate($tracks): |
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5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
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48 ## Hi-C Track |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
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49 #if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option": |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
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changeset
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50 #for $counter_matrix, $data_matrix in enumerate($track.track_file_style_conditional.matrix_h5_cooler_multiple): |
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c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
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51 [hic_section_${counter}_${counter_matrix}] |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
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52 #set ext = $data_matrix.extension |
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c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
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53 file = ${counter}_${counter_matrix}.$ext |
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0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
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54 file_type = hic_matrix |
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5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
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55 #if $track.track_file_style_conditional.title: |
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0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
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56 title = $track.track_file_style_conditional.title |
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5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
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57 #else: |
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0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
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58 title = $data_matrix.name |
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5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
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59 #end if |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
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60 #if $track.track_file_style_conditional.depth: |
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0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
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61 depth = $track.track_file_style_conditional.depth |
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5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
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62 #end if |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
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63 #if $track.track_file_style_conditional.colormap: |
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2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
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64 colormap = $track.track_file_style_conditional.colormap |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
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65 #end if |
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5cec5fb749f0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf"
iuc
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66 #if $track.track_file_style_conditional.min_value != "": |
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0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
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67 min_value = $track.track_file_style_conditional.min_value |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
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68 #end if |
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5cec5fb749f0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf"
iuc
parents:
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69 #if $track.track_file_style_conditional.max_value != "": |
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0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
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70 max_value = $track.track_file_style_conditional.max_value |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
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71 #end if |
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0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
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72 transform = $track.track_file_style_conditional.transform |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
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73 #if $track.track_file_style_conditional.height_matrix != "": |
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0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
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74 height = $track.track_file_style_conditional.height_matrix |
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5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
75 #end if |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
76 #if $track.track_file_style_conditional.show_masked_bins: |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
77 show_masked_bins = $track.track_file_style_conditional.show_masked_bins |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
78 #end if |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
79 #if $track.track_file_style_conditional.invert_orientation: |
|
2
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
80 orientation = inverted |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
81 #end if |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
82 #if $track.track_file_style_conditional.scale_factor: |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
83 scale_factor = $track.track_file_style_conditional.scale_factor |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
84 #end if |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
85 rasterize = $track.track_file_style_conditional.rasterize |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
86 ## If a boundary file is given a new section needs to be written: |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
87 #if str($track.track_file_style_conditional.boundaries_file) != "None": |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
88 #if len($track.track_file_style_conditional.boundaries_file)>$counter_matrix: |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
89 #set boundary_file = $track.track_file_style_conditional.boundaries_file[$counter_matrix] |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
90 #else: |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
91 #set boundary_file = $track.track_file_style_conditional.boundaries_file[0] |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
92 #end if |
|
2
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
93 [tads_${counter}_${counter_matrix}] |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
94 file = $boundary_file |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
95 file_type = domains |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
96 border_color = black |
|
2
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
97 color = none |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
98 overlay_previous = share-y |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
99 #end if |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
100 ## If spacer is asked a new section is created: |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
101 #if $track.track_file_style_conditional.spacer_height != "": |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
102 [spacer] |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
103 height = $track.track_file_style_conditional.spacer_height |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
104 #end if |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
105 #end for |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
106 #end if |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
107 |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
108 ## Chrom_state track |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
109 #if $track.track_file_style_conditional.track_file_style_selector == "chrom_states_option": |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
110 #for $data_bed in $track.track_file_style_conditional.track_input_bed: |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
111 [chrom states_$counter] |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
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112 file = $data_bed |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
113 #if $track.track_file_style_conditional.title: |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
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114 title = $track.track_file_style_conditional.title |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
115 #else: |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
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116 title = $data_bed.name |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
117 #end if |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
118 #if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb": |
|
2
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
119 color = bed_rgb |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
120 #elif $track.track_file_style_conditional.color_bed.color: |
|
2
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
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121 color = $track.track_file_style_conditional.color_bed.color |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
122 #end if |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
123 #if $track.track_file_style_conditional.border_color_bed.border_color_bed_select == 'manually': |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
124 border_color = $track.track_file_style_conditional.border_color_bed.color |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
125 #else |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
126 border_color = $track.track_file_style_conditional.border_color_bed.border_color_bed_select |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
127 #end if |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
128 display = collapsed |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
129 #if $track.track_file_style_conditional.height_chrom: |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
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|
130 height = $track.track_file_style_conditional.height_chrom |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
131 #end if |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
132 line_width = $track.track_file_style_conditional.line_width |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
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133 file_type = bed |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
134 ## If spacer is asked a new section is created: |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
135 #if $track.track_file_style_conditional.spacer_height != "": |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
136 [spacer] |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
137 height = $track.track_file_style_conditional.spacer_height |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
138 #end if |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
139 #end for |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
140 #end if |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
141 |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
142 ## Gene/gtf track |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
143 #if $track.track_file_style_conditional.track_file_style_selector == "gene_track_option": |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
144 #for $counter_bed, $data_bed in enumerate($track.track_file_style_conditional.track_input_bed): |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
145 [genes_${counter}_${counter_bed}] |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
146 #set ext = $data_bed.extension |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
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|
147 file = ${counter}_${counter_bed}.$ext |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
148 #if $ext == 'gtf': |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
149 prefered_name = $track.track_file_style_conditional.bed_style.bed_advanced.gtf.prefered_name |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
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150 merge_transcripts = $track.track_file_style_conditional.bed_style.bed_advanced.gtf.merge_transcripts |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
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151 #end if |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
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152 #if $track.track_file_style_conditional.title: |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
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153 title = $track.track_file_style_conditional.title |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
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154 #elif $track.track_file_style_conditional.overlay_select == 'no': |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
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155 title = $data_bed.name |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
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156 #end if |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
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157 #if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb": |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
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158 color = bed_rgb |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
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159 #elif $track.track_file_style_conditional.color_bed.color: |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
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changeset
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160 color = $track.track_file_style_conditional.color_bed.color |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
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161 #end if |
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7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
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162 #if $track.track_file_style_conditional.border_color_bed.border_color_bed_select == 'manually': |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
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163 border_color = $track.track_file_style_conditional.border_color_bed.color |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
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164 #else |
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326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
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changeset
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165 border_color = $track.track_file_style_conditional.border_color_bed.border_color_bed_select |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
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changeset
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166 #end if |
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7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
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167 style = $track.track_file_style_conditional.bed_style.bed_style_select |
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326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
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changeset
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168 #if $track.track_file_style_conditional.bed_style.bed_style_select == 'UCSC': |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
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169 arrow_interval = $track.track_file_style_conditional.bed_style.bed_advanced.arrow_interval |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
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170 #else: |
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326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
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171 height_utr = $track.track_file_style_conditional.bed_style.bed_advanced.height_utr |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
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172 #if $track.track_file_style_conditional.bed_style.bed_advanced.color_utr.color_utr_select == 'manually': |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
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173 color_utr = $track.track_file_style_conditional.bed_style.bed_advanced.color_utr.color |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
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174 #elif $track.track_file_style_conditional.bed_style.bed_advanced.color_utr.color_utr_select == 'bed_rgb': |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
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175 color_utr = bed_rgb |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
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176 #else: |
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326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
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177 #if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb": |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
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178 color_utr = bed_rgb |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
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179 #else: |
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326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
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180 color_utr = $track.track_file_style_conditional.color_bed.color |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
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181 #end if |
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326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
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182 #end if |
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326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
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183 #if $track.track_file_style_conditional.bed_style.bed_style_select == 'tssarrow' and $track.track_file_style_conditional.bed_style.bed_advanced.arrow_length != '': |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
184 arrow_length = $track.track_file_style_conditional.bed_style.bed_advanced.arrow_length |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
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185 #end if |
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326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
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186 #if $track.track_file_style_conditional.bed_style.bed_style_select == 'flybase': |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
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187 arrowhead_included = $track.track_file_style_conditional.bed_style.arrowhead_included |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
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188 #end if |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
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189 #end if |
|
2
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
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190 display = $track.track_file_style_conditional.display |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
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191 #if $track.track_file_style_conditional.height_bed: |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
192 height = $track.track_file_style_conditional.height_bed |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
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193 #end if |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
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194 labels = $track.track_file_style_conditional.labels.plot_labels |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
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195 #if $track.track_file_style_conditional.labels.plot_labels == 'true': |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
196 all_labels_inside = $track.track_file_style_conditional.labels.all_labels_inside |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
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197 labels_in_margin = $track.track_file_style_conditional.labels.labels_in_margin |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
198 #end if |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
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199 file_type = bed |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
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200 #if $track.track_file_style_conditional.fontsize: |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
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|
201 fontsize = $track.track_file_style_conditional.fontsize |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
202 #end if |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
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203 #if $track.track_file_style_conditional.bed_style.bed_advanced.gene_rows: |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
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204 gene_rows = $track.track_file_style_conditional.bed_style.bed_advanced.gene_rows |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
205 #end if |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
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206 global_max_row = $track.track_file_style_conditional.bed_style.bed_advanced.global_max_row |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
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207 max_labels = $track.track_file_style_conditional.bed_style.bed_advanced.max_labels |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
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208 line_width = $track.track_file_style_conditional.bed_style.bed_advanced.line_width |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
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209 #if $track.track_file_style_conditional.invert_orientation: |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
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210 orientation = inverted |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
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211 #end if |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
212 overlay_previous = $track.track_file_style_conditional.overlay_select |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
213 ## If spacer is asked a new section is created: |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
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214 #if $track.track_file_style_conditional.spacer_height != "": |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
215 [spacer] |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
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216 height = $track.track_file_style_conditional.spacer_height |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
217 #end if |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
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218 #end for |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
219 #end if |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
220 |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
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diff
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221 ## Link |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
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222 #if $track.track_file_style_conditional.track_file_style_selector == "link_track_option": |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
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223 [links_$counter] |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
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224 file = $track.track_file_style_conditional.track_input_link |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
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225 #if $track.track_file_style_conditional.title: |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
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226 title = $track.track_file_style_conditional.title |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
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227 #elif $track.track_file_style_conditional.overlay_select == 'no': |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
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228 title = $track.track_file_style_conditional.track_input_link.name |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
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229 #end if |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
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230 #if $track.track_file_style_conditional.height: |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
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231 height = $track.track_file_style_conditional.height |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
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232 #end if |
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6
5cec5fb749f0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf"
iuc
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233 #if $track.track_file_style_conditional.min_value != "": |
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5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
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234 min_value = $track.track_file_style_conditional.min_value |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
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235 #end if |
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6
5cec5fb749f0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf"
iuc
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236 #if $track.track_file_style_conditional.max_value != "": |
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5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
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237 max_value = $track.track_file_style_conditional.max_value |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
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238 #end if |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
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239 color = $track.track_file_style_conditional.color_link.color |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
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240 alpha = $track.track_file_style_conditional.alpha |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
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241 line_width = $track.track_file_style_conditional.line_width |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
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242 line_style = $track.track_file_style_conditional.line_style |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
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243 links_type = $track.track_file_style_conditional.links_type |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
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244 compact_arcs_level = $track.track_file_style_conditional.compact_arcs_level |
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326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
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245 #if $track.track_file_style_conditional.ylim != "": |
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326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
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246 ylim = $track.track_file_style_conditional.ylim |
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326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
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247 #end if |
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5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
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248 #if $track.track_file_style_conditional.invert_orientation: |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
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249 orientation = inverted |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
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250 #end if |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
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251 overlay_previous = $track.track_file_style_conditional.overlay_select |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
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252 file_type = links |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
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253 ## If spacer is asked a new section is created: |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
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254 #if $track.track_file_style_conditional.spacer_height != "": |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
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255 [spacer] |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
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256 height = $track.track_file_style_conditional.spacer_height |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
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257 #end if |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
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258 #end if |
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4
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
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259 |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
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260 ## Narrow peak |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
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261 #if $track.track_file_style_conditional.track_file_style_selector == "narrow_peak_track_option": |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
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262 #for $counter_narrow_peak, $data_narrow_peak in enumerate($track.track_file_style_conditional.track_input_narrow_peak): |
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4
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
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263 [narrow_peak_${counter}_${counter_narrow_peak}] |
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c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
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264 file = $data_narrow_peak |
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5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
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265 #if $track.track_file_style_conditional.title: |
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4
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
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266 title = $track.track_file_style_conditional.title |
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5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
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267 #elif $track.track_file_style_conditional.overlay_select == 'no': |
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4
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
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268 title = $data_narrow_peak.name |
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5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
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269 #end if |
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4
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
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270 color = $track.track_file_style_conditional.color |
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c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
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271 type = $track.track_file_style_conditional.display.display_selector |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
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272 use_summit = $track.track_file_style_conditional.display.use_summit |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
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273 #if $track.track_file_style_conditional.display.display_selector == "peak": |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
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274 show_data_range = $track.track_file_style_conditional.display.show_data |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
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275 #if $track.track_file_style_conditional.display.width_adjust: |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
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276 width_adjust = $track.track_file_style_conditional.display.width_adjust |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
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277 #end if |
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6
5cec5fb749f0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf"
iuc
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278 #if $track.track_file_style_conditional.display.min_value != "": |
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4
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
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279 min_value = $track.track_file_style_conditional.display.min_value |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
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280 #end if |
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6
5cec5fb749f0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf"
iuc
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281 #if $track.track_file_style_conditional.display.max_value != "": |
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4
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
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282 max_value = $track.track_file_style_conditional.display.max_value |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
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283 #end if |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
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284 #end if |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
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285 #if $track.track_file_style_conditional.height_narrow_peak: |
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4
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
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286 height = $track.track_file_style_conditional.height_narrow_peak |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
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287 #end if |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
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288 line_width = $track.track_file_style_conditional.line_width |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
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289 show_labels = $track.track_file_style_conditional.show_labels |
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4
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
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290 file_type = narrow_peak |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
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291 #if $track.track_file_style_conditional.fontsize: |
|
4
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
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292 fontsize = $track.track_file_style_conditional.fontsize |
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5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
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293 #end if |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
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294 #if $track.track_file_style_conditional.invert_orientation: |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
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295 orientation = inverted |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
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296 #end if |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
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297 overlay_previous = $track.track_file_style_conditional.overlay_select |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
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298 ## If spacer is asked a new section is created: |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
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299 #if $track.track_file_style_conditional.spacer_height != "": |
|
4
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
300 [spacer] |
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c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
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301 height = $track.track_file_style_conditional.spacer_height |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
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302 #end if |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
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303 #end for |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
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304 #end if |
|
4
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
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305 |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
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306 ## Bedgraph track |
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eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
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307 #if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_track_option": |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
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diff
changeset
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308 #for $data_bedgraph in $track.track_file_style_conditional.track_input_bedgraph: |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
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309 [bedgraph_$counter] |
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2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
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310 file = $data_bedgraph |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
311 #if $track.track_file_style_conditional.title: |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
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312 title = $track.track_file_style_conditional.title |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
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313 #elif $track.track_file_style_conditional.overlay_select == "no": |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
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314 title = $data_bedgraph.name |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
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315 #end if |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
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316 #if $track.track_file_style_conditional.color: |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
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317 color = $track.track_file_style_conditional.color |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
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318 #end if |
|
2
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
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319 alpha = $track.track_file_style_conditional.alpha |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
320 #if $track.track_file_style_conditional.color_negative.color_negative_select == "true": |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
321 negative_color = $track.track_file_style_conditional.color_negative.color |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
322 #end if |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
323 #if $track.track_file_style_conditional.height_bedgraph: |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
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324 height = $track.track_file_style_conditional.height_bedgraph |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
325 #end if |
|
6
5cec5fb749f0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf"
iuc
parents:
5
diff
changeset
|
326 #if $track.track_file_style_conditional.min_value != "": |
|
2
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
327 min_value = $track.track_file_style_conditional.min_value |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
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328 #end if |
|
6
5cec5fb749f0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf"
iuc
parents:
5
diff
changeset
|
329 #if $track.track_file_style_conditional.max_value != "": |
|
2
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
330 max_value = $track.track_file_style_conditional.max_value |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
331 #end if |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
332 show_data_range = $track.track_file_style_conditional.show_data |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
333 nans_to_zeros = $track.track_file_style_conditional.nans_to_zeros |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
334 use_middle = $track.track_file_style_conditional.use_middle |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
335 #set $columns = len(open(str($track.track_file_style_conditional.track_input_bedgraph)).readline().split('\t')) |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
336 #if $columns > 4: |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
337 file_type = bedgraph_matrix |
|
2
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
338 type = lines |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
339 #else: |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
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340 file_type = bedgraph |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
341 #if $track.track_file_style_conditional.type_conditional.type_selector == 'fill_option': |
|
2
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
342 type = fill |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
343 #elif $track.track_file_style_conditional.type_conditional.type_selector == 'line_option': |
|
2
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
344 type = line:$track.track_file_style_conditional.type_conditional.width_line |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
345 #elif $track.track_file_style_conditional.type_conditional.type_selector == 'point_option': |
|
2
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
346 type = points:$track.track_file_style_conditional.type_conditional.width_point |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
347 #end if |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
348 #end if |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
349 #if $track.track_file_style_conditional.invert_orientation: |
|
2
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
350 orientation = inverted |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
351 #end if |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
352 overlay_previous = $track.track_file_style_conditional.overlay_select |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
353 ## If spacer is asked a new section is created: |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
354 #if $track.track_file_style_conditional.spacer_height != "": |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
355 [spacer] |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
356 height = $track.track_file_style_conditional.spacer_height |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
357 #end if |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
358 #end for |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
359 #end if |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
360 |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
361 ## Bigwig tracks |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
362 #if $track.track_file_style_conditional.track_file_style_selector == "bigwig_track_option": |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
363 #for $data_bigwig in $track.track_file_style_conditional.track_input_bigwig: |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
364 [bigwig_$counter] |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
365 file = $data_bigwig |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
366 #if $track.track_file_style_conditional.title: |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
367 title = $track.track_file_style_conditional.title |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
368 #elif $track.track_file_style_conditional.overlay_select == "no": |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
369 title = $data_bigwig.name |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
370 #end if |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
371 #if $track.track_file_style_conditional.color: |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
372 color = $track.track_file_style_conditional.color |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
373 #end if |
|
2
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
374 alpha = $track.track_file_style_conditional.alpha |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
375 #if $track.track_file_style_conditional.color_negative.color_negative_select == "true": |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
376 negative_color = $track.track_file_style_conditional.color_negative.color |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
377 #end if |
|
6
5cec5fb749f0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf"
iuc
parents:
5
diff
changeset
|
378 #if $track.track_file_style_conditional.min_value != "": |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
379 min_value = $track.track_file_style_conditional.min_value |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
380 #end if |
|
6
5cec5fb749f0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf"
iuc
parents:
5
diff
changeset
|
381 #if $track.track_file_style_conditional.max_value != "": |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
382 max_value = $track.track_file_style_conditional.max_value |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
383 #end if |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
384 height = $track.track_file_style_conditional.height_bigwig |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
385 summary_method = $track.track_file_style_conditional.reading_bw_conditional.summary |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
386 nans_to_zeros = $track.track_file_style_conditional.reading_bw_conditional.nans_to_zeros |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
387 #if $track.track_file_style_conditional.reading_bw_conditional.number_of_bins: |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
388 number_of_bins = $track.track_file_style_conditional.reading_bw_conditional.number_of_bins |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
389 #end if |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
390 #if $track.track_file_style_conditional.type_conditional.type_selector == 'fill_option': |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
391 type = fill |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
392 #elif $track.track_file_style_conditional.type_conditional.type_selector == 'line_option': |
|
2
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
393 type = line:$track.track_file_style_conditional.type_conditional.width_line |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
394 #elif $track.track_file_style_conditional.type_conditional.type_selector == 'point_option': |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
395 type = points:$track.track_file_style_conditional.type_conditional.width_point |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
396 #end if |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
397 show_data_range = $track.track_file_style_conditional.show_data |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
398 file_type = bigwig |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
399 #if $track.track_file_style_conditional.invert_orientation: |
|
2
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
400 orientation = inverted |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
401 #end if |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
402 overlay_previous = $track.track_file_style_conditional.overlay_select |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
403 ## If spacer is asked a new section is created: |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
404 #if $track.track_file_style_conditional.spacer_height != "": |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
405 [spacer] |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
406 height = $track.track_file_style_conditional.spacer_height |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
407 #end if |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
408 #end for |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
409 #end if |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
410 |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
411 ## bedgraph_matrix |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
412 #if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_matrix_track_option": |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
413 #for $data_bedgraph_matrix in $track.track_file_style_conditional.track_input_bedgraph_matrix: |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
414 [bedgraph_matrix_$counter] |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
415 file = $data_bedgraph_matrix |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
416 #if $track.track_file_style_conditional.title: |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
417 title = $track.track_file_style_conditional.title |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
418 #else: |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
419 title = $data_bedgraph_matrix.name |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
420 #end if |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
421 #if $track.track_file_style_conditional.height_bedgraph: |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
422 height = $track.track_file_style_conditional.height_bedgraph |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
423 #end if |
|
6
5cec5fb749f0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf"
iuc
parents:
5
diff
changeset
|
424 #if $track.track_file_style_conditional.min_value != "": |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
425 min_value = $track.track_file_style_conditional.min_value |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
426 #end if |
|
6
5cec5fb749f0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf"
iuc
parents:
5
diff
changeset
|
427 #if $track.track_file_style_conditional.max_value != "": |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
428 max_value = $track.track_file_style_conditional.max_value |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
429 #end if |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
430 type = $track.track_file_style_conditional.type.type_selector |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
431 file_type = bedgraph_matrix |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
432 #if $track.track_file_style_conditional.type.type_selector == 'lines': |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
433 show_data_range = $track.track_file_style_conditional.type.show_data |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
434 plot_horizontal_lines = $track.track_file_style_conditional.type.plot_horizontal_lines |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
435 pos_score_in_bin = $track.track_file_style_conditional.type.pos_score_in_bin |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
436 #else |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
437 colormap = $track.track_file_style_conditional.type.colormap |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
438 #end if |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
439 #if $track.track_file_style_conditional.invert_orientation: |
|
2
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
440 orientation = inverted |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
441 #end if |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
442 ## If spacer is asked a new section is created: |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
443 #if $track.track_file_style_conditional.spacer_height != "": |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
444 [spacer] |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
445 height = $track.track_file_style_conditional.spacer_height |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
446 #end if |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
447 #end for |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
448 #end if |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
449 |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
450 ## Vlines: |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
451 #if $track.track_file_style_conditional.track_file_style_selector == "vlines_track_option": |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
452 [vlines_$counter] |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
453 file = $track.track_file_style_conditional.track_input_bed_single |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
454 type = vlines |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
455 #end if |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
456 |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
457 ## Hlines: |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
458 #if $track.track_file_style_conditional.track_file_style_selector == "hlines_track_option": |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
459 [hlines_$counter] |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
460 #if $track.track_file_style_conditional.title: |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
461 title = $track.track_file_style_conditional.title |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
462 #end if |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
463 #if $track.track_file_style_conditional.height: |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
464 height = $track.track_file_style_conditional.height |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
465 #end if |
|
6
5cec5fb749f0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf"
iuc
parents:
5
diff
changeset
|
466 #if $track.track_file_style_conditional.min_value != "": |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
467 min_value = $track.track_file_style_conditional.min_value |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
468 #end if |
|
6
5cec5fb749f0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf"
iuc
parents:
5
diff
changeset
|
469 #if $track.track_file_style_conditional.max_value != "": |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
470 max_value = $track.track_file_style_conditional.max_value |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
471 #end if |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
472 y_values = $track.track_file_style_conditional.y_values |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
473 show_data_range = $track.track_file_style_conditional.show_data |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
474 color = $track.track_file_style_conditional.color |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
475 alpha = $track.track_file_style_conditional.alpha |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
476 line_width = $track.track_file_style_conditional.line_width |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
477 line_style = $track.track_file_style_conditional.line_style |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
478 #if $track.track_file_style_conditional.invert_orientation: |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
479 orientation = inverted |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
480 #end if |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
481 overlay_previous = $track.track_file_style_conditional.overlay_select |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
482 file_type = hlines |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
483 ## If spacer is asked a new section is created: |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
484 #if $track.track_file_style_conditional.spacer_height != "": |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
485 [spacer] |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
486 height = $track.track_file_style_conditional.spacer_height |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
487 #end if |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
488 #end if |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
489 |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
490 ## Spacer |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
491 #if $track.track_file_style_conditional.track_file_style_selector == "spacer_option": |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
492 [spacer] |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
493 #if $track.track_file_style_conditional.title: |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
494 title = $track.track_file_style_conditional.title |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
495 #end if |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
496 #if $track.track_file_style_conditional.spacer_height != "": |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
497 height = $track.track_file_style_conditional.spacer_height |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
498 #end if |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
499 #end if |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
500 |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
501 ## Xaxis: |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
502 #if $track.track_file_style_conditional.track_file_style_selector == "xaxis_option": |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
503 [x-axis] |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
504 #if $track.track_file_style_conditional.title: |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
505 title = $track.track_file_style_conditional.title |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
506 #end if |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
507 #if $track.track_file_style_conditional.fontsize != "": |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
508 fontsize = $track.track_file_style_conditional.fontsize |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
509 #end if |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
510 where = $track.track_file_style_conditional.xaxis_where |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
511 ## If spacer is asked a new section is created: |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
512 #if $track.track_file_style_conditional.spacer_height != "": |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
513 [spacer] |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
514 height = $track.track_file_style_conditional.spacer_height |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
515 #end if |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
516 #end if |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
517 |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
518 ## Scale bar: |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
519 #if $track.track_file_style_conditional.track_file_style_selector == "scale_bar_option": |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
520 [scale_bar] |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
521 #if $track.track_file_style_conditional.title: |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
522 title = $track.track_file_style_conditional.title |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
523 #end if |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
524 #if $track.track_file_style_conditional.color != "": |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
525 color = $track.track_file_style_conditional.color |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
526 #end if |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
527 alpha = $track.track_file_style_conditional.alpha |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
528 line_width = $track.track_file_style_conditional.line_width |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
529 #if $track.track_file_style_conditional.x_center != "": |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
530 x_center = $track.track_file_style_conditional.x_center |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
531 #end if |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
532 #if $track.track_file_style_conditional.size != "": |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
533 size = $track.track_file_style_conditional.size |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
534 #end if |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
535 where = $track.track_file_style_conditional.sb_where |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
536 #if $track.track_file_style_conditional.fontsize != "": |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
537 fontsize = $track.track_file_style_conditional.fontsize |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
538 #end if |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
539 file_type = scalebar |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
540 ## If spacer is asked a new section is created: |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
541 #if $track.track_file_style_conditional.spacer_height != "": |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
542 [spacer] |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
543 height = $track.track_file_style_conditional.spacer_height |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
544 #end if |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
545 #end if |
|
1
0ea86f6bf2a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit f834c2a294c002123ef0613dc703aca00201b5bf
iuc
parents:
0
diff
changeset
|
546 #end for |
|
0ea86f6bf2a1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit f834c2a294c002123ef0613dc703aca00201b5bf
iuc
parents:
0
diff
changeset
|
547 </configfile> |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
548 </configfiles> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
549 <inputs> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
550 <!--Arguments for pgt--> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
551 <param argument="--region" type="text" label="Region of the genome to limit the operation" optional="false" |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
552 help="The format is chr:start-end. Also valid is just to specify a chromosome, for example chr10:10-500" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
553 <section name="global_args" title="Configure figure parameters" expanded="False"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
554 <param argument="--title" type="text" label="Plot title" help="If set, you may need to start by a spacer track"/> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
555 <param argument="--fontsize" type="integer" label="Font size for the labels of the plot" value="12"/> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
556 <param argument="--dpi" type="integer" label="Resolution (dpi)" value="72" |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
557 help="Resolution for the image in case the ouput is a raster graphics image (e.g png, jpg)"/> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
558 <param argument="--trackLabelFraction" type="float" label="Proportion of space dedicated to track labels" value="0.05" |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
559 min="0" max="1"/> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
560 <param argument="--trackLabelHAlign" type="select" label="Horizontal alignment of track labels"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
561 <option value="left" selected="True">left</option> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
562 <option value="right">right</option> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
563 <option value="center">center</option> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
564 </param> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
565 </section> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
566 <!--Info to build the config file--> |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
567 <repeat name="tracks" min="1" title="Include tracks in your plot" |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
568 help="Tracks can be of different filetypes. E.g BED, HiC-Matrix, BigWig or BedGraph. |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
569 The order you add them represent the order they will be plotted from top to bottom."> |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
570 <conditional name="track_file_style_conditional"> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
571 <param name="track_file_style_selector" type="select" label="Choose style of the track"> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
572 <option value="hic_matrix_option">TAD visualization</option> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
573 <option value="chrom_states_option">Chromatine states</option> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
574 <option value="bedgraph_matrix_track_option">TAD score</option> |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
575 <option value="gene_track_option">Gene track / Bed track</option> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
576 <option value="link_track_option">Link track</option> |
|
4
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
577 <option value="narrow_peak_track_option">NarrowPeak track</option> |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
578 <option value="bigwig_track_option">Bigwig track</option> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
579 <option value="bedgraph_track_option">Bedgraph track </option> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
580 <option value="bedgraph_matrix_track_option">Bedgraph matrix track</option> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
581 <option value="vlines_track_option">Vlines track</option> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
582 <option value="hlines_track_option">Hlines track</option> |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
583 <option value="spacer_option">Spacer</option> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
584 <option value="xaxis_option">X-axis</option> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
585 <option value="scale_bar_option">Scale bar track</option> |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
586 </param> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
587 <when value="hic_matrix_option"> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
588 <expand macro="plot_title" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
589 <expand macro="matrix_h5_cooler_multiple_macro" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
590 |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
591 <param name="colormap" type="select" label="Color map to use for the heatmap" help="Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
592 <option value="RdYlBu_r">RdYlBu reversed</option> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
593 <expand macro="colormap_macro"/> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
594 </param> |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
595 <param name="depth" type="integer" value="8000000" optional="True" label="Depth" /> |
|
2
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
596 <expand macro="minmax_macro" /> |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
597 <param name="transform" type="select" label="Plot the transformed value"> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
598 <option value="log1p" selected="True" >log1p</option> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
599 <option value="log">log</option> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
600 <option value="-log">-log</option> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
601 <option value="no">no transformation</option> |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
602 |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
603 </param> |
|
2
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
604 <param name="height_matrix" type="float" value="" optional="True" label="height"/> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
605 <param name="show_masked_bins" type="boolean" truevalue="true" falsevalue="false" checked="false" |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
606 label="Show masked bins" /> |
|
6
5cec5fb749f0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf"
iuc
parents:
5
diff
changeset
|
607 <param name="boundaries_file" type="data" optional="True" format="bed" label="Boundaries file" multiple="True"/> |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
608 <param name="scale_factor" type="float" value="1.0" optional="True" label="Scale factor" help="if the values in the matrix need to be scaled the following parameter can be used" /> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
609 <param name="rasterize" type="boolean" truevalue="true" falsevalue="false" checked="true" |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
610 label="Rasterize the heatmap" /> |
|
2
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
611 <expand macro="inverted_macro" /> |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
612 <expand macro="spacer_macro" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
613 |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
614 </when> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
615 <when value="chrom_states_option"> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
616 <expand macro="plot_title" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
617 <expand macro="track_input_bed_macro" /> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
618 <conditional name="color_bed"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
619 <param name="color_bed_select" type="select" label="Define color:"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
620 <option value="manually" selected="True">manually</option> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
621 <option value="bed_rgb">From the 9th field</option> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
622 <option value="colormap">From the 5th field (score)</option> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
623 </param> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
624 <when value="manually"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
625 <param name="color" type="color" value="#000000" label="Color of track" optional="True" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
626 </when> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
627 <when value="bed_rgb" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
628 <when value="colormap"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
629 <param name="color" type="select" label="Color map to use for the scores" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
630 <expand macro="colormap_macro" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
631 </param> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
632 </when> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
633 </conditional> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
634 <expand macro="border_color_bed_macro" /> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
635 <param name="line_width" type="float" value="0.5" label="width of lines" /> |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
636 <param name="height_chrom" type="float" value="1.5" optional="True" label="height"/> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
637 <param name="labels" type="boolean" truevalue="true" falsevalue="false" checked="true" |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
638 label="Plot labels" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
639 <expand macro="spacer_macro" /> |
|
2
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
640 |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
641 </when> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
642 <when value="gene_track_option"> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
643 <expand macro="plot_title" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
644 |
|
2
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
645 <expand macro="track_input_bed_gtf_macro" /> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
646 <conditional name="color_bed"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
647 <param name="color_bed_select" type="select" label="Define color:"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
648 <option value="manually" selected="True">manually</option> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
649 <option value="bed_rgb">From the 9th field</option> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
650 <option value="colormap">From the 5th field (score)</option> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
651 </param> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
652 <when value="manually"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
653 <param name="color" type="color" value="#000000" label="Color of track" optional="True" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
654 </when> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
655 <when value="bed_rgb" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
656 <when value="colormap"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
657 <param name="color" type="select" label="Color map to use for the scores" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
658 <expand macro="colormap_macro" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
659 </param> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
660 </when> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
661 </conditional> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
662 <expand macro="border_color_bed_macro" /> |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
663 <param name="height_bed" type="float" value="1.5" optional="True" label="height"/> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
664 <conditional name="labels"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
665 <param name="plot_labels" type="select" label="Plot labels"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
666 <option value="true" selected="True">yes</option> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
667 <option value="false">no</option> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
668 </param> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
669 <when value="true"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
670 <param name="all_labels_inside" type="boolean" truevalue="true" falsevalue="false" checked="false" |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
671 label="Put all labels inside the plotted region" |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
672 help="Put labels on the left of the region if the region ends after the plotted region."/> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
673 <param name="labels_in_margin" type="boolean" truevalue="true" falsevalue="false" checked="false" |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
674 label="Allow to put labels in the right margin" |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
675 help="Put labels in the margin if the region ends after the plotted region."/> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
676 </when> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
677 <when value="false"/> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
678 </conditional> |
|
2
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
679 <param name="display" type="select" label="display to use"> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
680 <option value="stacked" selected="True">stacked (no overlap even with the label)</option> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
681 <option value="interleaved">interleaved (everything on 2 lines)</option> |
|
2
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
682 <option value="collapsed">collapsed (everything on 1 line)</option> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
683 <option value="triangles">triangles (plot triangles between start and end)</option> |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
684 </param> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
685 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" /> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
686 <conditional name="bed_style"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
687 <param name="bed_style_select" type="select" label="Bed style"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
688 <option value="flybase" selected="True">flybase (blocks with arrow at extremities)</option> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
689 <option value="UCSC">UCSC (blocks with arrows in introns)</option> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
690 <option value="tssarrow">tssarrow (blocks with arrow above at beginning)</option> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
691 </param> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
692 <when value="flybase"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
693 <param name="arrowhead_included" type="boolean" truevalue="true" falsevalue="false" checked="false" |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
694 label="Include the arrowhead in the bed interval:" |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
695 help="When set to False, the arrow indicating the orientation of the interval is plotted outside of the interval."/> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
696 <section name="bed_advanced" title="Configure other bed parameters" expanded="False"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
697 <expand macro="utr_macro" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
698 <expand macro="bed_advanced_macro" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
699 </section> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
700 </when> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
701 <when value="UCSC"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
702 <section name="bed_advanced" title="Configure other bed parameters" expanded="False"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
703 <param name="arrow_interval" type="integer" value="2" min="0" label="interval between 2 arrows on introns in UCSC style"/> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
704 <expand macro="bed_advanced_macro" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
705 </section> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
706 </when> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
707 <when value="tssarrow"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
708 <section name="bed_advanced" title="Configure other bed parameters" expanded="False"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
709 <param name="arrow_length" type="integer" optional="true" label="arrow length" help="the length of the arrow in bp (default is 4% of the plotted region)"/> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
710 <expand macro="utr_macro" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
711 <expand macro="bed_advanced_macro" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
712 </section> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
713 </when> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
714 </conditional> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
715 <expand macro="overlay_macro" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
716 <expand macro="inverted_macro" /> |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
717 <expand macro="spacer_macro" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
718 |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
719 </when> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
720 <when value="link_track_option"> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
721 <expand macro="plot_title" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
722 <expand macro="track_input_link_macro" /> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
723 <conditional name="color_link"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
724 <param name="color_link_select" type="select" label="Define color:"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
725 <option value="manually" selected="True">manually</option> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
726 <option value="colormap">From the 7th field (score)</option> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
727 </param> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
728 <when value="manually"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
729 <param name="color" type="color" value="#000000" label="Color of track" optional="True" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
730 </when> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
731 <when value="colormap"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
732 <param name="color" type="select" label="Color map to use for the scores" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
733 <expand macro="colormap_macro" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
734 </param> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
735 </when> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
736 </conditional> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
737 <expand macro="lines_macro" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
738 <param name="links_type" type="select" label="Representation of the link:"> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
739 <option value="arcs" selected="True">arcs (a line between the centers of the 2 regions)</option> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
740 <option value="triangles">triangles</option> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
741 <option value="loops">loops (a rectangle highlighting the intersection)</option> |
|
6
5cec5fb749f0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf"
iuc
parents:
5
diff
changeset
|
742 </param> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
743 <param name="compact_arcs_level" type="select" label="Height of arcs and triangles:"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
744 <option value="0" selected="True">default (proportional to distance)</option> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
745 <option value="1">compacted (the height is proportional to the square root of the distance)</option> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
746 <option value="2">highly compacted (the height is the same for all distances)</option> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
747 </param> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
748 <param name="ylim" type="float" optional="True" label="ylim" help="To be able to see small arcs when big arcs exists, you can set the upper y limit. The unit is bp. This corresponds to the longest arc you will see not truncated."/> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
749 <param name="height" type="float" value="1.5" optional="True" label="height"/> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
750 <expand macro="minmax_macro" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
751 <expand macro="overlay_macro" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
752 <expand macro="inverted_macro" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
753 <expand macro="spacer_macro" /> |
|
6
5cec5fb749f0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf"
iuc
parents:
5
diff
changeset
|
754 </when> |
|
4
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
755 <when value="narrow_peak_track_option"> |
|
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
756 <expand macro="plot_title" /> |
|
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
757 <expand macro="track_input_narrow_peak_macro" /> |
|
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
758 <param name="color" type="color" value="#000000" label="Color of track" optional="True" /> |
|
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
759 <param name="height_narrow_peak" type="float" value="1.5" optional="True" label="height"/> |
|
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
760 <conditional name="display"> |
|
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
761 <param name="display_selector" type="select" label="display to use"> |
|
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
762 <option value="peak" selected="True">peak: Draw a peak shape from start, end, summit, height</option> |
|
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
763 <option value="box">box: Draw a box</option> |
|
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
764 </param> |
|
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
765 <when value="peak"> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
766 <param name="use_summit" type="boolean" truevalue="true" falsevalue="false" checked="true" |
|
4
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
767 optional="True" label="Use summit information to make the curve." /> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
768 <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false" |
|
4
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
769 label="Show visualization of data range" /> |
|
6
5cec5fb749f0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf"
iuc
parents:
5
diff
changeset
|
770 <param name="width_adjust" type="float" value="1.5" optional="True" |
|
4
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
771 label="Factor to change the width of the curve."/> |
|
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
772 <expand macro="minmax_macro" /> |
|
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
773 </when> |
|
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
774 <when value="box"> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
775 <param name="use_summit" type="boolean" truevalue="true" falsevalue="false" checked="true" |
|
4
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
776 optional="True" label="Plot a vertical bar at the summit position." /> |
|
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
777 </when> |
|
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
778 </conditional> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
779 <param name="line_width" type="float" value="1" label="width of lines" /> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
780 <param name="show_labels" type="boolean" truevalue="true" falsevalue="false" checked="true" |
|
4
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
781 label="Plot labels (name, p-val, q-val)" /> |
|
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
782 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" /> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
783 <expand macro="overlay_macro" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
784 <expand macro="inverted_macro" /> |
|
4
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
785 <expand macro="spacer_macro" /> |
|
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
786 |
|
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
787 </when> |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
788 <when value="bedgraph_track_option"> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
789 <expand macro="plot_title" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
790 <expand macro="track_input_bedgraph_macro" /> |
|
2
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
791 <expand macro="color_coverage_macro" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
792 <expand macro="minmax_macro" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
793 <param name="height_bedgraph" type="float" value="1.5" optional="True" label="height"/> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
794 <expand macro="type_coverage_macro" /> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
795 <param name="nans_to_zeros" type="boolean" truevalue="true" falsevalue="false" checked="false" |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
796 label="NAN's to zeros" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
797 <param name="use_middle" type="boolean" truevalue="true" falsevalue="false" checked="false" |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
798 label="Use middle: Instead of using start and end, use the middle of intervals (useful for 4C-seq tracks)." /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
799 <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show visualization of data range" /> |
|
2
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
800 <expand macro="inverted_macro" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
801 <expand macro="overlay_macro" /> |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
802 <expand macro="spacer_macro" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
803 </when> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
804 <when value="bigwig_track_option"> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
805 <expand macro="plot_title" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
806 |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
807 <expand macro="track_input_bigwig_macro" /> |
|
2
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
808 <expand macro="color_coverage_macro" /> |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
809 |
|
2
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
810 <expand macro="minmax_macro" /> |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
811 |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
812 <param name="height_bigwig" type="float" value="1.5" optional="True" label="height"/> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
813 <section name="reading_bw_conditional" title="Configure bigwig parameters" expanded="False"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
814 <param name="summary" type="select" label="Summary method"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
815 <option value="mean" selected="True">mean=mean value</option> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
816 <option value="min">min=minimum value</option> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
817 <option value="max">max=maximum value</option> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
818 <option value="coverage">coverage=number of covered bases</option> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
819 <option value="std">std=standard deviation</option> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
820 </param> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
821 <param name="number_of_bins" type="integer" value="" optional="True" label="Number of bins" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
822 <param name="nans_to_zeros" type="boolean" truevalue="true" falsevalue="false" checked="false" |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
823 label="NAN's to zeros" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
824 </section> |
|
2
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
825 <expand macro="type_coverage_macro" /> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
826 <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show visualization of data range"/> |
|
2
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
827 <expand macro="inverted_macro" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
828 <expand macro="overlay_macro" /> |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
829 <expand macro="spacer_macro" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
830 |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
831 </when> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
832 |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
833 <when value="bedgraph_matrix_track_option"> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
834 <expand macro="plot_title" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
835 |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
836 <expand macro="track_input_bedgraph_matrix_macro" /> |
|
2
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
837 <expand macro="minmax_macro" /> |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
838 |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
839 <param name="height_bedgraph" type="float" value="1.5" optional="True" label="height"/> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
840 |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
841 <conditional name="type"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
842 <param name="type_selector" type="select" label="type of plotting"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
843 <option value="lines" selected="True">lines: each column in the bedgraph will be a line and a mean line will be added</option> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
844 <option value="matrix">matrix: each column in the bedgraph will be a raw in the matrix</option> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
845 </param> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
846 <when value="lines"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
847 <param name="plot_horizontal_lines" type="boolean" truevalue="true" falsevalue="false" checked="false" |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
848 label="Plot an horizontal line at 0 when type is lines" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
849 <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false" |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
850 label="Show visualization of data range" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
851 <param name="pos_score_in_bin" type="select" label="Position of the score with respect to bin start and end"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
852 <option value="center" selected="True">Center</option> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
853 <option value="block">Block (draw a horizontal line between start and end)</option> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
854 </param> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
855 </when> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
856 <when value="matrix"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
857 <param name="colormap" type="select" label="colormap"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
858 <option value="viridis">Viridis</option> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
859 <expand macro="colormap_macro" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
860 </param> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
861 </when> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
862 </conditional> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
863 |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
864 |
|
2
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
865 <expand macro="inverted_macro" /> |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
866 <expand macro="spacer_macro" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
867 |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
868 </when> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
869 <when value="vlines_track_option"> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
870 <expand macro="track_input_bed_single_macro" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
871 </when> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
872 <when value="hlines_track_option"> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
873 <expand macro="plot_title" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
874 <param name="y_values" type="text" value="10, 200" label="Values where horizontal lines should be plotted separated by comma"/> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
875 <param name="color" type="color" value="#000000" label="Color of line(s)" optional="True" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
876 <expand macro="lines_macro" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
877 <param name="height" type="float" value="1.5" optional="True" label="height"/> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
878 <expand macro="minmax_macro" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
879 <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show visualization of data range"/> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
880 <expand macro="inverted_macro" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
881 <expand macro="overlay_macro" /> |
|
6
5cec5fb749f0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf"
iuc
parents:
5
diff
changeset
|
882 <expand macro="spacer_macro" /> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
883 </when> |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
884 <when value="spacer_option"> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
885 <expand macro="plot_title" /> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
886 <param name="spacer_height" type="float" value="" optional="True" |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
887 label="Height of the spacer."/> |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
888 </when> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
889 <when value="xaxis_option"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
890 <expand macro="plot_title" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
891 <param name="fontsize" type="float" optional="True" |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
892 label="Fontsize of the x-axis."/> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
893 <param name="xaxis_where" type="select" label="chromosome name and coordinates position relative to the axis"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
894 <option value="bottom" selected="True">below</option> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
895 <option value="top">above</option> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
896 </param> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
897 <expand macro="spacer_macro" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
898 </when> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
899 <when value="scale_bar_option"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
900 <expand macro="plot_title" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
901 <param name="color" type="color" label="Color of the scale bar" optional="True" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
902 <param name="alpha" type="float" value="1" min="0" max="1" label="level of transparency (alpha)" help="1 is opaque and 0 is totally transparent"/> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
903 <param name="line_width" type="float" value="0.5" label="width of lines"/> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
904 <param name="x_center" type="integer" label="coordinate where the scale bar should be plotted (center)" optional="True" |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
905 help="If not set it will be in the middle of the plotted area."/> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
906 <param name="size" type="integer" label="size of the scale bar" optional="True" |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
907 help="If not set it will be the higher number that begins with 1, 2 or 5 followed by 0s that is less than half the plotted area."/> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
908 <param name="sb_where" type="select" label="where the size of the scale bar should appear relative to the bar"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
909 <option value="left" selected="True">left</option> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
910 <option value="right">right</option> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
911 <option value="bottom">below</option> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
912 <option value="top">above</option> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
913 </param> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
914 <param name="fontsize" type="float" optional="True" |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
915 label="Fontsize of the size of the scale bar."/> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
916 <expand macro="spacer_macro" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
917 </when> |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
918 </conditional> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
919 </repeat> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
920 <param name="image_file_format" type="select" label="Image output format"> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
921 <option value="png">png</option> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
922 <option value="svg">svg</option> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
923 </param> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
924 </inputs> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
925 <outputs> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
926 <data format="png" name="outFileName" from_work_dir="plot" label="${tool.name} on [${on_string}]: Plot"> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
927 <change_format> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
928 <when input="image_file_format" value="png" format="png" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
929 <when input="image_file_format" value="svg" format="svg" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
930 </change_format> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
931 </data> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
932 </outputs> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
933 <tests> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
934 <!--test 1--> |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
935 <test> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
936 <param name="region" value="chrX:3000000-3500000"/> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
937 <repeat name="tracks"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
938 <conditional name="track_file_style_conditional"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
939 <param name="track_file_style_selector" value="xaxis_option" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
940 <param name="xaxis_where" value="top" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
941 </conditional> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
942 </repeat> |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
943 <repeat name="tracks"> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
944 <conditional name="track_file_style_conditional"> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
945 <param name="track_file_style_selector" value="hic_matrix_option" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
946 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
947 <param name="title" value="Kc DpnII (Li et al. 2015)" /> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
948 <!--<param name="colormap" value="RdYlBu_r" />--> |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
949 <param name="depth" value="200000" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
950 <param name="transform" value="log1p" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
951 <param name="boundaries_file" value="domains.bed" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
952 </conditional> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
953 </repeat> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
954 <repeat name="tracks"> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
955 <conditional name="track_file_style_conditional"> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
956 <param name="track_file_style_selector" value="spacer_option" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
957 <param name="spacer_height" value="0.05" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
958 </conditional> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
959 </repeat> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
960 <repeat name="tracks"> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
961 <conditional name="track_file_style_conditional"> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
962 <param name="track_file_style_selector" value="chrom_states_option" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
963 <param name="track_input_bed" value="tad_classification.bed" ftype="bed" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
964 <param name="title" value="TAD state" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
965 <param name="height_chrom" value="0.5" /> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
966 <param name="labels" value="false" /> |
|
2
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
967 <conditional name="color_bed"> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
968 <param name="color_bed_select" value="bed_rgb" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
969 </conditional> |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
970 </conditional> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
971 </repeat> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
972 <repeat name="tracks"> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
973 <conditional name="track_file_style_conditional"> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
974 <param name="track_file_style_selector" value="bedgraph_matrix_track_option" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
975 <param name="track_input_bedgraph_matrix" value="tad_score.gz" ftype="bedgraph" /> |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
976 <param name="title" value="TAD separation score (Ramirez et al.)" /> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
977 <conditional name="type"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
978 <param name="type_selector" value="matrix" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
979 <!--<param name="colormap" value="viridis" />--> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
980 </conditional> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
981 <param name="height_bedgraph" value="10" /> |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
982 </conditional> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
983 </repeat> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
984 <repeat name="tracks"> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
985 <conditional name="track_file_style_conditional"> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
986 <param name="track_file_style_selector" value="spacer_option" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
987 <param name="spacer_height" value="1" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
988 </conditional> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
989 </repeat> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
990 <repeat name="tracks"> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
991 <conditional name="track_file_style_conditional"> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
992 <param name="track_file_style_selector" value="bedgraph_track_option" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
993 <param name="track_input_bedgraph" value="bedgraph_chrx_2e6_5e6.bg" ftype="bedgraph" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
994 <param name="title" value="bedgraph" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
995 <param name="height_bedgraph" value="4" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
996 <param name="color" value="blue" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
997 </conditional> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
998 </repeat> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
999 <repeat name="tracks"> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1000 <conditional name="track_file_style_conditional"> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1001 <param name="track_file_style_selector" value="bigwig_track_option" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1002 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1003 <param name="title" value="rep 1 test fill" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1004 <param name="height_bigwig" value="4" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1005 <param name="color" value="blue" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1006 <conditional name="type_conditional"> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1007 <param name="type_selector" value="fill_option" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1008 </conditional> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1009 </conditional> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1010 </repeat> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1011 <repeat name="tracks"> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1012 <conditional name="track_file_style_conditional"> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1013 <param name="track_file_style_selector" value="bigwig_track_option" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1014 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1015 <param name="title" value="rep 1 test line" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1016 <param name="height_bigwig" value="4" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1017 <param name="color" value="red" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1018 <conditional name="type_conditional"> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1019 <param name="type_selector" value="line_option" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1020 <param name="width_line" value="1" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1021 </conditional> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1022 </conditional> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1023 </repeat> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1024 <repeat name="tracks"> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1025 <conditional name="track_file_style_conditional"> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1026 <param name="track_file_style_selector" value="bigwig_track_option" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1027 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1028 <param name="title" value="rep 1 test lw=0.2" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1029 <param name="height_bigwig" value="4" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1030 <param name="color" value="red" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1031 <conditional name="type_conditional"> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1032 <param name="type_selector" value="line_option" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1033 <param name="width_line" value="0.1" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1034 |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1035 </conditional> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1036 </conditional> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1037 </repeat> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1038 <repeat name="tracks"> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1039 <conditional name="track_file_style_conditional"> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1040 <param name="track_file_style_selector" value="bigwig_track_option" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1041 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1042 <param name="title" value="rep 1 test point:0.5" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1043 <param name="height_bigwig" value="4" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1044 <param name="color" value="black" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1045 <conditional name="type_conditional"> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1046 <param name="type_selector" value="point_option" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1047 <param name="width_point" value="0.5" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1048 |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1049 </conditional> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1050 </conditional> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1051 </repeat> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1052 <repeat name="tracks"> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1053 <conditional name="track_file_style_conditional"> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1054 <param name="track_file_style_selector" value="spacer_option" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1055 <param name="spacer_height" value="0.5" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1056 </conditional> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1057 </repeat> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1058 <repeat name="tracks"> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1059 <conditional name="track_file_style_conditional"> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1060 <param name="track_file_style_selector" value="gene_track_option" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1061 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1062 <param name="title" value="genes" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1063 <param name="height_bed" value="5" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1064 <param name="fontsize" value="10" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1065 </conditional> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1066 </repeat> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1067 <repeat name="tracks"> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1068 <conditional name="track_file_style_conditional"> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1069 <param name="track_file_style_selector" value="spacer_option" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1070 <param name="spacer_height" value="1" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1071 </conditional> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1072 </repeat> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1073 <repeat name="tracks"> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1074 <conditional name="track_file_style_conditional"> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1075 <param name="track_file_style_selector" value="gene_track_option" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1076 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1077 <param name="title" value="max num rows 3" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1078 <param name="height_bed" value="3" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1079 <param name="fontsize" value="8" /> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1080 <conditional name="bed_style"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1081 <section name="bed_advanced"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1082 <param name="gene_rows" value="3" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1083 </section> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1084 </conditional> |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1085 </conditional> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1086 </repeat> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1087 <repeat name="tracks"> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1088 <conditional name="track_file_style_conditional"> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1089 <param name="track_file_style_selector" value="spacer_option" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1090 <param name="spacer_height" value="1" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1091 </conditional> |
|
2
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1092 </repeat> |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1093 <repeat name="tracks"> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1094 <conditional name="track_file_style_conditional"> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1095 <param name="track_file_style_selector" value="gene_track_option" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1096 <param name="track_input_bed" value="dm3_genes.bed6.gz" ftype="bed" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1097 <param name="title" value="bed6 global max row" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1098 <param name="height_bed" value="20" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1099 <param name="fontsize" value="10" /> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1100 <conditional name="bed_style"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1101 <section name="bed_advanced"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1102 <param name="global_max_row" value="true" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1103 </section> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1104 </conditional> |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1105 </conditional> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1106 </repeat> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1107 <repeat name="tracks"> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1108 <conditional name="track_file_style_conditional"> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1109 <param name="track_file_style_selector" value="vlines_track_option" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1110 <param name="track_input_bed_single" value="domains.bed" ftype="bed" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1111 </conditional> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1112 </repeat> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1113 <param name="image_file_format" value="png" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1114 <output name="outFileName" file="master_TADs_plot.png" ftype="png" compare="sim_size" delta="35000" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1115 </test> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1116 <!--test 2--> |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1117 <test> |
|
2
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1118 <param name="region" value="chrX:3000000-3500000"/> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1119 <repeat name="tracks"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1120 <conditional name="track_file_style_conditional"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1121 <param name="track_file_style_selector" value="xaxis_option" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1122 <param name="xaxis_where" value="top" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1123 </conditional> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1124 </repeat> |
|
2
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1125 <repeat name="tracks"> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1126 <conditional name="track_file_style_conditional"> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1127 <param name="track_file_style_selector" value="bigwig_track_option" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1128 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw,bigwig_chrx_2e6_5e6.bw" ftype="bigwig" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1129 <param name="title" value="rep 1 test line" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1130 <param name="height_bigwig" value="4" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1131 <param name="color" value="red" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1132 <conditional name="type_conditional"> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1133 <param name="type_selector" value="line_option" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1134 <param name="width_line" value="1" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1135 </conditional> |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1136 </conditional> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1137 </repeat> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1138 <repeat name="tracks"> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1139 <conditional name="track_file_style_conditional"> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1140 <param name="track_file_style_selector" value="bigwig_track_option" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1141 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1142 <param name="title" value="nans_to_zeros" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1143 <param name="height_bigwig" value="4" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1144 <param name="color" value="blue" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1145 <section name="reading_bw_conditional"> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1146 <param name="nans_to_zeros" value="true" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1147 </section> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1148 <param name="show_data" value="true" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1149 <conditional name="type_conditional"> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1150 <param name="type_selector" value="line_option" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1151 <param name="width_line" value="1" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1152 </conditional> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1153 </conditional> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1154 </repeat> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1155 <repeat name="tracks"> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1156 <conditional name="track_file_style_conditional"> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1157 <param name="track_file_style_selector" value="hlines_track_option" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1158 <param name="title" value="" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1159 <param name="color" value="orange" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1160 <param name="y_values" value="50" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1161 <param name="line_width" value="2" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1162 <param name="line_style" value="dashed" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1163 <param name="overlay_select" value="share-y" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1164 </conditional> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1165 </repeat> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1166 <repeat name="tracks"> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1167 <conditional name="track_file_style_conditional"> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1168 <param name="track_file_style_selector" value="hlines_track_option" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1169 <param name="title" value="hlines" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1170 <param name="color" value="purple" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1171 <param name="y_values" value="0, 10, 20, 100" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1172 <param name="min_value" value="12" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1173 <param name="show_data" value="true" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1174 <param name="invert_orientation" value="true" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1175 </conditional> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1176 </repeat> |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1177 <param name="image_file_format" value="png" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1178 <output name="outFileName" file="bigwig_multiple.png" ftype="png" compare="sim_size" delta="35000" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
1179 </test> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1180 <!--test 3--> |
|
2
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1181 <test> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1182 <param name="region" value="chrX:3000000-3500000"/> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1183 <repeat name="tracks"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1184 <conditional name="track_file_style_conditional"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1185 <param name="track_file_style_selector" value="xaxis_option" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1186 <param name="xaxis_where" value="top" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1187 </conditional> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1188 </repeat> |
|
2
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1189 <repeat name="tracks"> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1190 <conditional name="track_file_style_conditional"> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1191 <param name="track_file_style_selector" value="hic_matrix_option" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1192 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1193 <param name="title" value="Kc DpnII (Li et al. 2015) log1p" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1194 <param name="colormap" value="RdYlBu_r" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1195 <param name="depth" value="200000" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1196 <param name="transform" value="log1p" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1197 <param name="boundaries_file" value="domains.bed" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1198 </conditional> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1199 </repeat> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1200 <repeat name="tracks"> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1201 <conditional name="track_file_style_conditional"> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1202 <param name="track_file_style_selector" value="chrom_states_option" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1203 <param name="track_input_bed" value="tad_classification.bed" ftype="bed" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1204 <param name="title" value="TAD state" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1205 <param name="height_chrom" value="0.5" /> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1206 <param name="labels" value="false" /> |
|
2
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1207 <conditional name="color_bed"> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1208 <param name="color_bed_select" value="bed_rgb" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1209 </conditional> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1210 </conditional> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1211 </repeat> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1212 <repeat name="tracks"> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1213 <conditional name="track_file_style_conditional"> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1214 <param name="track_file_style_selector" value="hic_matrix_option" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1215 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1216 <param name="title" value="Kc DpnII (Li et al. 2015) inverted no transform" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1217 <param name="colormap" value="Reds" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1218 <param name="depth" value="200000" /> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1219 <param name="transform" value="no" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1220 <param name="invert_orientation" value="true" /> |
|
2
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1221 <param name="min_value" value="5" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1222 <param name="max_value" value="70" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1223 </conditional> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1224 </repeat> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1225 <repeat name="tracks"> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1226 <conditional name="track_file_style_conditional"> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1227 <param name="track_file_style_selector" value="spacer_option" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1228 <param name="spacer_height" value="1" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1229 </conditional> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1230 </repeat> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1231 <repeat name="tracks"> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1232 <conditional name="track_file_style_conditional"> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1233 <param name="track_file_style_selector" value="bedgraph_track_option" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1234 <param name="track_input_bedgraph" value="test_with_neg_values.bg.gz" ftype="bedgraph" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1235 <param name="title" value="bedgraph with negative values" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1236 <param name="height_bedgraph" value="4" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1237 <param name="color" value="black" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1238 <conditional name="color_negative"> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1239 <param name="color_negative_select" value="true" /> |
|
2
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1240 <param name="color" value="red" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1241 </conditional> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1242 <conditional name="type_conditional"> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1243 <param name="type_selector" value="fill_option" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1244 </conditional> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1245 </conditional> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1246 </repeat> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1247 <repeat name="tracks"> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1248 <conditional name="track_file_style_conditional"> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1249 <param name="track_file_style_selector" value="bedgraph_track_option" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1250 <param name="track_input_bedgraph" value="bedgraph_chrx_2e6_5e6.bg" ftype="bedgraph" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1251 <param name="title" value="bedgraph" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1252 <param name="height_bedgraph" value="4" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1253 <param name="color" value="blue" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1254 <conditional name="type_conditional"> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1255 <param name="type_selector" value="fill_option" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1256 </conditional> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1257 </conditional> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1258 </repeat> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1259 <repeat name="tracks"> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1260 <conditional name="track_file_style_conditional"> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1261 <param name="track_file_style_selector" value="bigwig_track_option" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1262 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1263 <param name="title" value="rep 1 test fill" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1264 <param name="height_bigwig" value="4" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1265 <param name="color" value="blue" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1266 <conditional name="type_conditional"> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1267 <param name="type_selector" value="fill_option" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1268 </conditional> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1269 </conditional> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1270 </repeat> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1271 <repeat name="tracks"> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1272 <conditional name="track_file_style_conditional"> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1273 <param name="track_file_style_selector" value="bigwig_track_option" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1274 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1275 <param name="title" value="(red points/width=5/max value/100 bins) overlayed with (dark red line/min value/30000 bins) overlayed with (black line/min value)" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1276 <param name="height_bigwig" value="10" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1277 <param name="color" value="red" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1278 <conditional name="type_conditional"> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1279 <param name="type_selector" value="point_option" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1280 <param name="width_point" value="5" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1281 </conditional> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1282 <section name="reading_bw_conditional"> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1283 <param name="summary" value="max"/> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1284 <param name="number_of_bins" value="100"/> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1285 </section> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1286 </conditional> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1287 </repeat> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1288 <repeat name="tracks"> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1289 <conditional name="track_file_style_conditional"> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1290 <param name="track_file_style_selector" value="bigwig_track_option" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1291 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1292 <param name="height_bigwig" value="10" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1293 <param name="color" value="#c00000" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1294 <conditional name="type_conditional"> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1295 <param name="type_selector" value="line_option" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1296 </conditional> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1297 <section name="reading_bw_conditional"> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1298 <param name="summary" value="min"/> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1299 </section> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1300 <param name="overlay_select" value="share-y" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1301 </conditional> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1302 </repeat> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1303 <repeat name="tracks"> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1304 <conditional name="track_file_style_conditional"> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1305 <param name="track_file_style_selector" value="bigwig_track_option" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1306 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1307 <param name="height_bigwig" value="10" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1308 <param name="color" value="black" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1309 <conditional name="type_conditional"> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1310 <param name="type_selector" value="line_option" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1311 </conditional> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1312 <section name="reading_bw_conditional"> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1313 <param name="summary" value="min"/> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1314 <param name="number_of_bins" value="30000"/> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1315 </section> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1316 <param name="overlay_select" value="share-y" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1317 <param name="spacer_height" value="1" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1318 </conditional> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1319 </repeat> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1320 <repeat name="tracks"> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1321 <conditional name="track_file_style_conditional"> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1322 <param name="track_file_style_selector" value="gene_track_option" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1323 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1324 <param name="title" value="genes in ucsc" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1325 <param name="height_bed" value="5" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1326 <param name="fontsize" value="10" /> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1327 <conditional name="bed_style"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1328 <param name="bed_style_select" value="UCSC"/> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1329 </conditional> |
|
2
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1330 </conditional> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1331 </repeat> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1332 <repeat name="tracks"> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1333 <conditional name="track_file_style_conditional"> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1334 <param name="track_file_style_selector" value="gene_track_option" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1335 <param name="track_input_bed" value="dm3_genes.bed6.gz" ftype="bed" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1336 <param name="title" value="bed6 global max row color from score" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1337 <param name="height_bed" value="20" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1338 <param name="fontsize" value="10" /> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1339 <conditional name="bed_style"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1340 <section name="bed_advanced"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1341 <param name="global_max_row" value="true" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1342 </section> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1343 </conditional> |
|
2
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1344 <conditional name="color_bed"> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1345 <param name="color_bed_select" value="colormap" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1346 <param name="color" value="RdYlBu_r" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1347 </conditional> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1348 </conditional> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1349 </repeat> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1350 <repeat name="tracks"> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1351 <conditional name="track_file_style_conditional"> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1352 <param name="track_file_style_selector" value="gene_track_option" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1353 <param name="track_input_bed" value="domains.bed" ftype="bed" /> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1354 <param name="title" value="domains.bed using the 9th field for colors interleaved border=red" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1355 <param name="height_bed" value="2" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1356 <param name="fontsize" value="10" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1357 <conditional name="color_bed"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1358 <param name="color_bed_select" value="bed_rgb" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1359 </conditional> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1360 <conditional name="border_color_bed"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1361 <param name="border_color_bed_select" value="manually" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1362 <param name="color" value="red" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1363 </conditional> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1364 <conditional name="labels"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1365 <param name="plot_labels" value="false" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1366 </conditional> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1367 <param name="display" value="interleaved" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1368 </conditional> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1369 </repeat> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1370 <repeat name="tracks"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1371 <conditional name="track_file_style_conditional"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1372 <param name="track_file_style_selector" value="gene_track_option" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1373 <param name="track_input_bed" value="domains.bed" ftype="bed" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1374 <param name="title" value="domains.bed using the 9th field for colors interleaved border=bed_rgb" /> |
|
2
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1375 <param name="height_bed" value="2" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1376 <param name="fontsize" value="10" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1377 <conditional name="color_bed"> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1378 <param name="color_bed_select" value="bed_rgb" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1379 </conditional> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1380 <conditional name="border_color_bed"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1381 <param name="border_color_bed_select" value="bed_rgb" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1382 </conditional> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1383 <conditional name="labels"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1384 <param name="plot_labels" value="false" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1385 </conditional> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1386 <param name="display" value="interleaved" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1387 </conditional> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1388 </repeat> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1389 <repeat name="tracks"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1390 <conditional name="track_file_style_conditional"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1391 <param name="track_file_style_selector" value="gene_track_option" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1392 <param name="track_input_bed" value="domains.bed" ftype="bed" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1393 <param name="title" value="domains.bed using the 9th field for colors interleaved border=none" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1394 <param name="height_bed" value="2" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1395 <param name="fontsize" value="10" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1396 <conditional name="color_bed"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1397 <param name="color_bed_select" value="bed_rgb" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1398 </conditional> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1399 <conditional name="border_color_bed"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1400 <param name="border_color_bed_select" value="none" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1401 </conditional> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1402 <conditional name="labels"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1403 <param name="plot_labels" value="false" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1404 </conditional> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1405 <param name="display" value="interleaved" /> |
|
2
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1406 </conditional> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1407 </repeat> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1408 <param name="image_file_format" value="png" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1409 <output name="outFileName" file="master_TADs_BW_plot.png" ftype="png" compare="sim_size" delta="35000" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1410 </test> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1411 <!--test 4--> |
|
2
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1412 <test> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1413 <param name="region" value="X:2700000-3100000"/> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1414 <repeat name="tracks"> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1415 <conditional name="track_file_style_conditional"> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1416 <param name="track_file_style_selector" value="bigwig_track_option" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1417 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1418 <param name="title" value="(bigwig color=blue 2000 bins) overlayed with (bigwig mean color=red alpha = 0.5 max over 300 bins)" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1419 <param name="height_bigwig" value="7" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1420 <param name="color" value="#00b0f0" /> |
|
4
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
1421 <section name="reading_bw_conditional"> |
|
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
1422 <param name="number_of_bins" value="2000"/> |
|
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
1423 </section> |
|
2
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1424 </conditional> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1425 </repeat> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1426 <repeat name="tracks"> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1427 <conditional name="track_file_style_conditional"> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1428 <param name="track_file_style_selector" value="bigwig_track_option" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1429 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1430 <param name="title" value="" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1431 <param name="color" value="#ff0000" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1432 <param name="alpha" value="0.5" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1433 <param name="summary" value="max" /> |
|
4
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
1434 <section name="reading_bw_conditional"> |
|
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
1435 <param name="number_of_bins" value="300"/> |
|
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
1436 </section> |
|
2
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1437 <param name="overlay_select" value="share-y"/> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1438 </conditional> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1439 </repeat> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1440 <repeat name="tracks"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1441 <conditional name="track_file_style_conditional"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1442 <param name="track_file_style_selector" value="xaxis_option" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1443 <param name="xaxis_where" value="bottom" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1444 </conditional> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1445 </repeat> |
|
2
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1446 <param name="image_file_format" value="png" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1447 <output name="outFileName" file="test_alpha.png" ftype="png" compare="sim_size" delta="35000" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1448 </test> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1449 <!--test 5--> |
|
2
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1450 <test> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1451 <param name="region" value="X:3000000-3300000"/> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1452 <repeat name="tracks"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1453 <conditional name="track_file_style_conditional"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1454 <param name="track_file_style_selector" value="xaxis_option" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1455 <param name="xaxis_where" value="top" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1456 </conditional> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1457 </repeat> |
|
2
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1458 <repeat name="tracks"> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1459 <conditional name="track_file_style_conditional"> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1460 <param name="track_file_style_selector" value="gene_track_option" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1461 <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1462 <param name="title" value="test" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1463 <param name="height_bed" value="10" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1464 <param name="color" value="#000000" /> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1465 <conditional name="bed_style"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1466 <param name="bed_style_select" value="UCSC"/> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1467 </conditional> |
|
2
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1468 <param name="spacer_height" value="1"/> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1469 </conditional> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1470 </repeat> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1471 <repeat name="tracks"> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1472 <conditional name="track_file_style_conditional"> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1473 <param name="track_file_style_selector" value="gene_track_option" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1474 <param name="track_input_bed" value="dm3_subset_BDGP5.78_asbed4.bed.gz" ftype="bed" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1475 <param name="title" value="test" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1476 <param name="height_bed" value="10" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1477 <param name="color" value="#000000" /> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1478 <conditional name="bed_style"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1479 <param name="bed_style_select" value="UCSC"/> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1480 </conditional> |
|
2
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1481 <param name="spacer_height" value="1"/> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1482 </conditional> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1483 </repeat> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1484 <param name="image_file_format" value="png" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1485 <output name="outFileName" file="test_gtf_bed4.png" ftype="png" compare="sim_size" delta="35000" /> |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
1486 </test> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1487 <!--test 6--> |
|
4
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
1488 <test> |
|
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
1489 <param name="region" value="X:2760000-2802000"/> |
|
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
1490 <repeat name="tracks"> |
|
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
1491 <conditional name="track_file_style_conditional"> |
|
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
1492 <param name="track_file_style_selector" value="narrow_peak_track_option" /> |
|
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
1493 <param name="title" value="box" /> |
|
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
1494 <param name="track_input_narrow_peak" value="test2.narrowPeak" ftype="encodepeak" /> |
|
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
1495 <param name="color" value="#9bbb59" /> |
|
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
1496 <param name="height_narrow_peak" value="4" /> |
|
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
1497 <conditional name="display"> |
|
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
1498 <param name="display_selector" value="box" /> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1499 <param name="use_summit" value="true" /> |
|
4
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
1500 </conditional> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1501 <param name="show_labels" value="true" /> |
|
4
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
1502 </conditional> |
|
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
1503 </repeat> |
|
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
1504 <repeat name="tracks"> |
|
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
1505 <conditional name="track_file_style_conditional"> |
|
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
1506 <param name="track_file_style_selector" value="narrow_peak_track_option" /> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1507 <param name="title" value="box line_width = 2" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1508 <param name="track_input_narrow_peak" value="test2.narrowPeak" ftype="encodepeak" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1509 <param name="color" value="#9bbb59" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1510 <param name="height_narrow_peak" value="4" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1511 <param name="line_width" value="2" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1512 <conditional name="display"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1513 <param name="display_selector" value="box" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1514 <param name="use_summit" value="true" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1515 </conditional> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1516 <param name="show_labels" value="true" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1517 </conditional> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1518 </repeat> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1519 <repeat name="tracks"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1520 <conditional name="track_file_style_conditional"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1521 <param name="track_file_style_selector" value="narrow_peak_track_option" /> |
|
4
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
1522 <param name="title" value="peak width 3" /> |
|
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
1523 <param name="track_input_narrow_peak" value="test2.narrowPeak" ftype="encodepeak" /> |
|
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
1524 <param name="color" value="#c0504d" /> |
|
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
1525 <param name="height_narrow_peak" value="4" /> |
|
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
1526 <conditional name="display"> |
|
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
1527 <param name="display_selector" value="peak" /> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1528 <param name="use_summit" value="true" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1529 <param name="show_data" value="true" /> |
|
4
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
1530 <param name="width_adjust" value="3" /> |
|
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
1531 <param name="max_value" value="50" /> |
|
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
1532 </conditional> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1533 <param name="show_labels" value="false" /> |
|
4
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
1534 <param name="spacer_height" value="0.5"/> |
|
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
1535 </conditional> |
|
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
1536 </repeat> |
|
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
1537 <repeat name="tracks"> |
|
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
1538 <conditional name="track_file_style_conditional"> |
|
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
1539 <param name="track_file_style_selector" value="narrow_peak_track_option" /> |
|
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
1540 <param name="title" value="peak no data range" /> |
|
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
1541 <param name="track_input_narrow_peak" value="test2.narrowPeak" ftype="encodepeak" /> |
|
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
1542 <param name="color" value="#000000" /> |
|
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
1543 <param name="height_narrow_peak" value="4" /> |
|
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
1544 <conditional name="display"> |
|
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
1545 <param name="display_selector" value="peak" /> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1546 <param name="use_summit" value="false" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1547 <param name="show_data" value="false" /> |
|
4
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
1548 </conditional> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1549 <param name="show_labels" value="true" /> |
|
4
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
1550 </conditional> |
|
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
1551 </repeat> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1552 <repeat name="tracks"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1553 <conditional name="track_file_style_conditional"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1554 <param name="track_file_style_selector" value="xaxis_option" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1555 <param name="xaxis_where" value="bottom" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1556 </conditional> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1557 </repeat> |
|
4
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
1558 <param name="image_file_format" value="png" /> |
|
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
1559 <output name="outFileName" file="test_narrowPeak.png" ftype="png" compare="sim_size" delta="35000" /> |
|
c237ba772225
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
iuc
parents:
3
diff
changeset
|
1560 </test> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1561 <!--test 7--> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1562 <test> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1563 <param name="region" value="chrX:3300000-3500000"/> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1564 <repeat name="tracks"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1565 <conditional name="track_file_style_conditional"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1566 <param name="track_file_style_selector" value="xaxis_option" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1567 <param name="xaxis_where" value="top" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1568 </conditional> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1569 </repeat> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1570 <repeat name="tracks"> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1571 <conditional name="track_file_style_conditional"> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1572 <param name="track_file_style_selector" value="gene_track_option" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1573 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1574 <param name="title" value="genes" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1575 <param name="height_bed" value="10" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1576 </conditional> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1577 </repeat> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1578 <repeat name="tracks"> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1579 <conditional name="track_file_style_conditional"> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1580 <param name="track_file_style_selector" value="gene_track_option" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1581 <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1582 <param name="title" value="gtf" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1583 <param name="height_bed" value="10" /> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1584 <conditional name="bed_style"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1585 <section name="bed_advanced"> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1586 <param name="height_utr" value="0.75"/> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1587 <conditional name="color_utr"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1588 <param name="color_utr_select" value="manually"/> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1589 <param name="color" value="#ff0000"/> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1590 </conditional> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1591 <section name ="gtf"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1592 <param name="prefered_name" value="gene_name"/> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1593 <param name="merge_transcripts" value="true"/> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1594 </section> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1595 </section> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1596 </conditional> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1597 </conditional> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1598 </repeat> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1599 <repeat name="tracks"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1600 <conditional name="track_file_style_conditional"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1601 <param name="track_file_style_selector" value="gene_track_option" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1602 <param name="track_input_bed" value="dm3_genes_withrgbandscore.bed.gz" ftype="bed" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1603 <param name="title" value="genes with scores" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1604 <param name="height_bed" value="10" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1605 <conditional name="color_bed"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1606 <param name="color_bed_select" value="colormap" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1607 <param name="color" value="cool_r" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1608 </conditional> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1609 </conditional> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1610 </repeat> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1611 <repeat name="tracks"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1612 <conditional name="track_file_style_conditional"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1613 <param name="track_file_style_selector" value="gene_track_option" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1614 <param name="track_input_bed" value="dm3_genes_withrgbandscore.bed.gz" ftype="bed" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1615 <param name="title" value="genes with utr as bed_rgb" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1616 <param name="height_bed" value="10" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1617 <conditional name="bed_style"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1618 <section name="bed_advanced"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1619 <conditional name="color_utr"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1620 <param name="color_utr_select" value="bed_rgb"/> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1621 </conditional> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1622 </section> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1623 </conditional> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1624 </conditional> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1625 </repeat> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1626 <repeat name="tracks"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1627 <conditional name="track_file_style_conditional"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1628 <param name="track_file_style_selector" value="gene_track_option" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1629 <param name="track_input_bed" value="dm3_genes_withrgbandscore.bed.gz" ftype="bed" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1630 <param name="title" value="genes with coding as bed_rgb - labels_in_margin" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1631 <param name="height_bed" value="10" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1632 <conditional name="color_bed"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1633 <param name="color_bed_select" value="bed_rgb" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1634 </conditional> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1635 <conditional name="labels"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1636 <param name="plot_labels" value="true" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1637 <param name="labels_in_margin" value="true" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1638 </conditional> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1639 </conditional> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1640 </repeat> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1641 <repeat name="tracks"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1642 <conditional name="track_file_style_conditional"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1643 <param name="track_file_style_selector" value="gene_track_option" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1644 <param name="track_input_bed" value="dm3_genes_withrgbandscore.bed.gz" ftype="bed" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1645 <param name="title" value="genes bed_rgb like - all_labels_inside" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1646 <param name="height_bed" value="10" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1647 <conditional name="color_bed"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1648 <param name="color_bed_select" value="bed_rgb" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1649 </conditional> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1650 <conditional name="bed_style"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1651 <section name="bed_advanced"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1652 <conditional name="color_utr"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1653 <param name="color_utr_select" value="like"/> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1654 </conditional> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1655 </section> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1656 </conditional> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1657 <conditional name="labels"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1658 <param name="plot_labels" value="true" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1659 <param name="all_labels_inside" value="true" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1660 </conditional> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1661 </conditional> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1662 </repeat> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1663 <param name="image_file_format" value="png" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1664 <output name="outFileName" file="test_gtf_flybase_param.png" ftype="png" compare="sim_size" delta="35000" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1665 </test> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1666 <!--test 8--> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1667 <test> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1668 <param name="region" value="chrX:3300000-3500000"/> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1669 <repeat name="tracks"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1670 <conditional name="track_file_style_conditional"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1671 <param name="track_file_style_selector" value="xaxis_option" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1672 <param name="xaxis_where" value="top" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1673 </conditional> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1674 </repeat> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1675 <repeat name="tracks"> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1676 <conditional name="track_file_style_conditional"> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1677 <param name="track_file_style_selector" value="gene_track_option" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1678 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1679 <param name="title" value="dm3_genes.bed" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1680 <param name="height_bed" value="10" /> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1681 <conditional name="bed_style"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1682 <param name="bed_style_select" value="UCSC"/> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1683 <section name="bed_advanced"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1684 <param name="global_max_row" value="true" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1685 <param name="max_labels" value="15" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1686 </section> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1687 </conditional> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1688 </conditional> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1689 </repeat> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1690 <repeat name="tracks"> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1691 <conditional name="track_file_style_conditional"> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1692 <param name="track_file_style_selector" value="gene_track_option" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1693 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1694 <param name="title" value="genes.bed.gz" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1695 <param name="height_bed" value="10" /> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1696 <conditional name="bed_style"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1697 <param name="bed_style_select" value="UCSC"/> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1698 <section name="bed_advanced"> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1699 <param name="arrow_interval" value="10"/> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1700 <param name="line_width" value="2"/> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1701 </section> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1702 </conditional> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1703 </conditional> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1704 </repeat> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1705 <param name="image_file_format" value="png" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1706 <output name="outFileName" file="test_ucsc_param.png" ftype="png" compare="sim_size" delta="35000" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1707 </test> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1708 <!--test 9--> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1709 <test> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1710 <param name="region" value="X:3133000-3138000"/> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1711 <repeat name="tracks"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1712 <conditional name="track_file_style_conditional"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1713 <param name="track_file_style_selector" value="xaxis_option" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1714 <param name="xaxis_where" value="top" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1715 </conditional> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1716 </repeat> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1717 <repeat name="tracks"> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1718 <conditional name="track_file_style_conditional"> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1719 <param name="track_file_style_selector" value="gene_track_option" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1720 <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1721 <param name="title" value="test" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1722 <param name="height_bed" value="10" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1723 <param name="spacer_height" value="1"/> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1724 </conditional> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1725 </repeat> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1726 <repeat name="tracks"> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1727 <conditional name="track_file_style_conditional"> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1728 <param name="track_file_style_selector" value="gene_track_option" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1729 <param name="track_input_bed" value="dm3_subset_BDGP5.78_asbed4.bed.gz" ftype="bed" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1730 <param name="title" value="test" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1731 <param name="height_bed" value="10" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1732 <conditional name="color_bed"> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1733 <param name="color_bed_select" value="manually" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1734 <param name="color" value="red" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1735 </conditional> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1736 <conditional name="bed_style"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1737 <param name="bed_style_select" value="UCSC"/> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1738 </conditional> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1739 <param name="spacer_height" value="1"/> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1740 </conditional> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1741 </repeat> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1742 <repeat name="tracks"> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1743 <conditional name="track_file_style_conditional"> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1744 <param name="track_file_style_selector" value="gene_track_option" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1745 <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1746 <param name="title" value="test" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1747 <param name="height_bed" value="10" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1748 <conditional name="color_bed"> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1749 <param name="color_bed_select" value="manually" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1750 <param name="color" value="red" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1751 </conditional> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1752 <param name="spacer_height" value="1"/> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1753 <conditional name="bed_style"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1754 <param name="arrowhead_included" value="true"/> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1755 </conditional> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1756 </conditional> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1757 </repeat> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1758 <repeat name="tracks"> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1759 <conditional name="track_file_style_conditional"> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1760 <param name="track_file_style_selector" value="vlines_track_option" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1761 <param name="track_input_bed_single" value="dm3_subset_BDGP5.78_asbed4.bed.gz" ftype="bed" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1762 </conditional> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1763 </repeat> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1764 <param name="image_file_format" value="png" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1765 <output name="outFileName" file="test_arrowhead_zoom.png" ftype="png" compare="sim_size" delta="35000" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1766 </test> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1767 <!--test 10--> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1768 <test> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1769 <param name="region" value="X:3340000-3380000"/> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1770 <repeat name="tracks"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1771 <conditional name="track_file_style_conditional"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1772 <param name="track_file_style_selector" value="xaxis_option" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1773 <param name="xaxis_where" value="top" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1774 </conditional> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1775 </repeat> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1776 <repeat name="tracks"> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1777 <conditional name="track_file_style_conditional"> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1778 <param name="track_file_style_selector" value="gene_track_option" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1779 <param name="track_input_bed" value="domains.bed" ftype="bed" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1780 <param name="height_bed" value="6" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1781 <conditional name="color_bed"> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1782 <param name="color_bed_select" value="manually" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1783 <param name="color" value="yellow" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1784 </conditional> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1785 <param name="display" value="triangles" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1786 <param name="spacer_height" value="1"/> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1787 </conditional> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1788 </repeat> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1789 <repeat name="tracks"> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1790 <conditional name="track_file_style_conditional"> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1791 <param name="track_file_style_selector" value="bedgraph_track_option" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1792 <param name="track_input_bedgraph" value="bedgraph_chrx_2e6_5e6.bg" ftype="bedgraph" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1793 <param name="title" value="bedgraph" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1794 <param name="height_bedgraph" value="4" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1795 <param name="color" value="blue" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1796 <conditional name="type_conditional"> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1797 <param name="type_selector" value="line_option" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1798 </conditional> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1799 </conditional> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1800 </repeat> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1801 <repeat name="tracks"> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1802 <conditional name="track_file_style_conditional"> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1803 <param name="track_file_style_selector" value="bedgraph_track_option" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1804 <param name="track_input_bedgraph" value="bedgraph_chrx_2e6_5e6.bg" ftype="bedgraph" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1805 <param name="title" value="bedgraph" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1806 <param name="height_bedgraph" value="4" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1807 <param name="color" value="blue" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1808 <param name="use_middle" value="true" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1809 <conditional name="type_conditional"> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1810 <param name="type_selector" value="line_option" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1811 </conditional> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1812 </conditional> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1813 </repeat> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1814 <param name="image_file_format" value="png" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1815 <output name="outFileName" file="test_middle_triangle.png" ftype="png" compare="sim_size" delta="35000" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1816 </test> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1817 <!--test 11--> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1818 <test> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1819 <param name="region" value="chrX:3250000-3400000"/> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1820 <repeat name="tracks"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1821 <conditional name="track_file_style_conditional"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1822 <param name="track_file_style_selector" value="xaxis_option" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1823 <param name="xaxis_where" value="top" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1824 </conditional> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1825 </repeat> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1826 <repeat name="tracks"> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1827 <conditional name="track_file_style_conditional"> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1828 <param name="track_file_style_selector" value="hic_matrix_option" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1829 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1830 <param name="title" value="Kc DpnII (Li et al. 2015)" /> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1831 <!--<param name="colormap" value="RdYlBu_r" />--> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1832 <param name="depth" value="100000" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1833 <param name="transform" value="log1p" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1834 <param name="show_masked_bins" value="true" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1835 <param name="scale_factor" value="2.0" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1836 </conditional> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1837 </repeat> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1838 <repeat name="tracks"> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1839 <conditional name="track_file_style_conditional"> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1840 <param name="track_file_style_selector" value="spacer_option" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1841 <param name="spacer_height" value="0.05" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1842 </conditional> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1843 </repeat> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1844 <repeat name="tracks"> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1845 <conditional name="track_file_style_conditional"> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1846 <param name="track_file_style_selector" value="bedgraph_matrix_track_option" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1847 <param name="track_input_bedgraph_matrix" value="tad_score.gz" ftype="bedgraph" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1848 <param name="title" value="TAD separation score (Ramirez et al.)" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1849 <param name="height_bedgraph" value="10" /> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1850 <conditional name="type"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1851 <param name="type_selector" value="lines" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1852 <param name="pos_score_in_bin" value="block" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1853 <param name="plot_horizontal_lines" value="true" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1854 <param name="show_data" value="true" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1855 </conditional> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1856 </conditional> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1857 </repeat> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1858 <repeat name="tracks"> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1859 <conditional name="track_file_style_conditional"> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1860 <param name="track_file_style_selector" value="bedgraph_matrix_track_option" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1861 <param name="track_input_bedgraph_matrix" value="tad_score.gz" ftype="bedgraph" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1862 <param name="title" value="TAD separation score (Ramirez et al.)" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1863 <param name="height_bedgraph" value="10" /> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1864 <conditional name="type"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1865 <param name="type_selector" value="lines" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1866 <param name="pos_score_in_bin" value="center" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1867 <param name="plot_horizontal_lines" value="false" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1868 </conditional> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1869 </conditional> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1870 </repeat> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1871 <param name="image_file_format" value="png" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1872 <output name="outFileName" file="test_TADs_bdgm.png" ftype="png" compare="sim_size" delta="35000" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1873 </test> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1874 <!--test 12--> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1875 <test> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1876 <param name="region" value="chrX:3000000-3300000"/> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1877 <repeat name="tracks"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1878 <conditional name="track_file_style_conditional"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1879 <param name="track_file_style_selector" value="xaxis_option" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1880 <param name="xaxis_where" value="top" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1881 </conditional> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1882 </repeat> |
|
5
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1883 <repeat name="tracks"> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1884 <conditional name="track_file_style_conditional"> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1885 <param name="track_file_style_selector" value="hic_matrix_option" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1886 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1887 <param name="title" value="Kc DpnII (Li et al. 2015)" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1888 <param name="colormap" value="Purples" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1889 <param name="depth" value="190000" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1890 <param name="transform" value="no" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1891 </conditional> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1892 </repeat> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1893 <repeat name="tracks"> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1894 <conditional name="track_file_style_conditional"> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1895 <param name="track_file_style_selector" value="link_track_option" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1896 <param name="track_input_link" value="test.arcs" ftype="bed" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1897 <param name="title" value="" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1898 <param name="line_width" value="10" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1899 <param name="links_type" value="loops" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1900 <conditional name="color_link"> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1901 <param name="color_link_select" value="manually" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1902 <param name="color" value="red" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1903 </conditional> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1904 <param name="overlay_select" value="share-y" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1905 </conditional> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1906 </repeat> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1907 <repeat name="tracks"> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1908 <conditional name="track_file_style_conditional"> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1909 <param name="track_file_style_selector" value="link_track_option" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1910 <param name="track_input_link" value="test.arcs" ftype="bed" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1911 <param name="title" value="" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1912 <param name="height" value="5" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1913 <conditional name="color_link"> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1914 <param name="color_link_select" value="colormap" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1915 <param name="color" value="hot" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1916 </conditional> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1917 <param name="max_value" value="5"/> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1918 <param name="invert_orientation" value="true" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1919 </conditional> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1920 </repeat> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1921 <param name="image_file_format" value="png" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1922 <output name="outFileName" file="test_link.png" ftype="png" compare="sim_size" delta="35000" /> |
|
eca03db4f612
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
iuc
parents:
4
diff
changeset
|
1923 </test> |
|
7
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1924 <!--test 13--> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1925 <test> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1926 <param name="region" value="chrX:3000000-3300000"/> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1927 <repeat name="tracks"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1928 <conditional name="track_file_style_conditional"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1929 <param name="track_file_style_selector" value="link_track_option" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1930 <param name="track_input_link" value="test.arcs" ftype="bed" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1931 <param name="title" value="default" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1932 <conditional name="color_link"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1933 <param name="color_link_select" value="manually" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1934 <param name="color" value="#000000" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1935 </conditional> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1936 </conditional> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1937 </repeat> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1938 <repeat name="tracks"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1939 <conditional name="track_file_style_conditional"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1940 <param name="track_file_style_selector" value="link_track_option" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1941 <param name="track_input_link" value="test.arcs" ftype="bed" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1942 <param name="title" value="ylim 20kb" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1943 <conditional name="color_link"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1944 <param name="color_link_select" value="manually" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1945 <param name="color" value="#000000" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1946 </conditional> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1947 <param name="ylim" value="20000" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1948 </conditional> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1949 </repeat> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1950 <repeat name="tracks"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1951 <conditional name="track_file_style_conditional"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1952 <param name="track_file_style_selector" value="link_track_option" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1953 <param name="track_input_link" value="test.arcs" ftype="bed" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1954 <param name="title" value="compacted" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1955 <conditional name="color_link"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1956 <param name="color_link_select" value="manually" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1957 <param name="color" value="#000000" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1958 </conditional> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1959 <param name="compact_arcs_level" value="1" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1960 </conditional> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1961 </repeat> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1962 <repeat name="tracks"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1963 <conditional name="track_file_style_conditional"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1964 <param name="track_file_style_selector" value="link_track_option" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1965 <param name="track_input_link" value="test.arcs" ftype="bed" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1966 <param name="title" value="highly compacted" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1967 <conditional name="color_link"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1968 <param name="color_link_select" value="manually" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1969 <param name="color" value="#000000" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1970 </conditional> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1971 <param name="compact_arcs_level" value="2" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1972 </conditional> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1973 </repeat> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1974 <param name="image_file_format" value="png" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1975 <output name="outFileName" file="test_link2.png" ftype="png" compare="sim_size" delta="35000" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1976 </test> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1977 <!--test 14--> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1978 <test> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1979 <param name="region" value="chrX:3000000-3300000"/> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1980 <section name="global_args"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1981 <param name="title" value="Scale bar"/> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1982 <param name="trackLabelFraction" value="0.5"/> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1983 <param name="trackLabelHAlign" value="center"/> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1984 </section> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1985 <repeat name="tracks"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1986 <conditional name="track_file_style_conditional"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1987 <param name="track_file_style_selector" value="spacer_option" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1988 <param name="spacer_height" value="1.0" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1989 </conditional> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1990 </repeat> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1991 <repeat name="tracks"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1992 <conditional name="track_file_style_conditional"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1993 <param name="track_file_style_selector" value="scale_bar_option" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1994 <param name="title" value="default" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1995 <param name="spacer_height" value="1"/> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1996 </conditional> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1997 </repeat> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1998 <repeat name="tracks"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
1999 <conditional name="track_file_style_conditional"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2000 <param name="track_file_style_selector" value="scale_bar_option" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2001 <param name="title" value="scalebar where = right x_center = 3200000 size = 100002 fontsize = 8 line_width =2 color = red alpha = 0.5" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2002 <param name="color" value="red"/> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2003 <param name="alpha" value="0.5"/> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2004 <param name="line_width" value="2"/> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2005 <param name="x_center" value="3200000"/> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2006 <param name="size" value="100002"/> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2007 <param name="sb_where" value="right"/> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2008 <param name="fontsize" value="8"/> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2009 <param name="spacer_height" value="4"/> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2010 </conditional> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2011 </repeat> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2012 <param name="image_file_format" value="png" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2013 <output name="outFileName" file="test_scale_bar.png" ftype="png" compare="sim_size" delta="35000" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2014 </test> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2015 <!--test 15--> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2016 <test> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2017 <param name="region" value="chrX:3300000-3500000"/> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2018 <repeat name="tracks"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2019 <conditional name="track_file_style_conditional"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2020 <param name="track_file_style_selector" value="xaxis_option" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2021 <param name="xaxis_where" value="bottom" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2022 </conditional> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2023 </repeat> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2024 <repeat name="tracks"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2025 <conditional name="track_file_style_conditional"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2026 <param name="track_file_style_selector" value="gene_track_option" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2027 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2028 <param name="title" value="flybase" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2029 <param name="height_bed" value="10" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2030 </conditional> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2031 </repeat> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2032 <repeat name="tracks"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2033 <conditional name="track_file_style_conditional"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2034 <param name="track_file_style_selector" value="gene_track_option" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2035 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2036 <param name="title" value="UCSC" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2037 <param name="height_bed" value="10" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2038 <conditional name="bed_style"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2039 <param name="bed_style_select" value="UCSC"/> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2040 <section name="bed_advanced"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2041 <param name="arrow_interval" value="10"/> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2042 </section> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2043 </conditional> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2044 </conditional> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2045 </repeat> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2046 <repeat name="tracks"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2047 <conditional name="track_file_style_conditional"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2048 <param name="track_file_style_selector" value="gene_track_option" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2049 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2050 <param name="title" value="tssarrow" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2051 <param name="height_bed" value="10" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2052 <conditional name="bed_style"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2053 <param name="bed_style_select" value="tssarrow"/> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2054 </conditional> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2055 </conditional> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2056 </repeat> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2057 <repeat name="tracks"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2058 <conditional name="track_file_style_conditional"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2059 <param name="track_file_style_selector" value="gene_track_option" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2060 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2061 <param name="title" value="tssarrow 5kb" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2062 <param name="height_bed" value="10" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2063 <conditional name="bed_style"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2064 <param name="bed_style_select" value="tssarrow"/> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2065 <section name="bed_advanced"> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2066 <param name="arrow_length" value="5000"/> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2067 </section> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2068 </conditional> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2069 </conditional> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2070 </repeat> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
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|
2071 <param name="image_file_format" value="png" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2072 <output name="outFileName" file="test_tssarrow.png" ftype="png" compare="sim_size" delta="35000" /> |
|
326a3db8d9d1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
iuc
parents:
6
diff
changeset
|
2073 </test> |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
2074 </tests> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
2075 <help><![CDATA[ |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
2076 |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
2077 pyGenomeTracks |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
2078 ============== |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
2079 |
|
2
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
2080 **pyGenomeTracks** is a visualization tool which aims to produce high-quality genome browser tracks that are highly customizable. |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
2081 Currently, it is possible to plot: |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
2082 |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
2083 - bigwig |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
2084 - bed (many options) |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
2085 - bedgraph |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
2086 - links (represented as arcs) |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
2087 - Hi-C matrices |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
2088 |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
2089 _________________ |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
2090 |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
2091 Usage |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
2092 ----- |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
2093 |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
2094 This tool takes various types of tracks as input: |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
2095 |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
2096 - **Chromatin states:** display blocks of different colors following a bed file. |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
2097 - **Gene track / Bed Track:** display genes or bed files. Labels like gene names can be toggled on or off. |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
2098 - **Bigwig track:** generic bigwig track plotting. |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
2099 - **Bedgraph track:** generic bedgraph track plotting. |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
2100 - **Bedgraph matrix track** is used to specifically plot bm files computed by HiCExplorer's ``hicFindTADs`` (TAD seperation scores). |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
2101 - **Vlines:** vertical lines drawn on top of all tracks following a bed file. It is used as a visual support where regions start / end over all tracks, for example to display TAD boundaries computed by HiCExplorer's ``hicFindTADs``. |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
2102 - **Spacer:** Add some space between two tracks. |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
2103 - **Hi-C tracks:** |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
2104 - **TAD vizualisation:** corrected Hi-C contact matrix to plot a contact heatmap. It is recommended to follow HiCExplorer's ``hicPlotMatrix`` instructions. Boundaries file can used, which is the output of HiCExplorer's ``hicFindTADs`` in bed format. If selected, TADs will be drawn directly on the contact heatmap. |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
2105 - **TAD score:** display TAD seperation score computed by HiCExplorer's ``hicFindTADs``. |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
2106 |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
2107 |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
2108 For each track, parameters for the color, the width or the font size can be defined. |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
2109 |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
2110 _________________ |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
2111 |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
2112 Output |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
2113 ------ |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
2114 |
|
2
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
2115 **pyGenomeTracks** output is similar to a genome browser screen-shot that besides the usual genes, and score data (like bigwig or bedgraph files) |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
2116 also contains Hi-C data. The plot is composed of tracks that need to be specified. |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
2117 Below is represented the 85 Mb to 110 Mb region from human chromosome 2 visualized using **pyGenomeTracks**. |
|
2
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
2118 TADs were computed by HiCExplorer's ``hicFindTADs``. The additional tracks added correspond to: |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
2119 TAD-separation score (as reported by HiCExplorer's ``hicFindTADs``), chromatin states, |
|
c171f2b7d76e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
iuc
parents:
1
diff
changeset
|
2120 principal component 1 (A/B compartment) computed using HiCExplorer's ``hicPCA``, ChIP-seq coverage for the H3K27ac mark, DNA methylation, and a gene track. |
|
0
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
2121 Data are from mouse cardiac myocytes, published by `Nothjunge et al. (2017)`_. |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
2122 |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
2123 .. image:: $PATH_TO_IMAGES/pyGenomeTracks.png |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
2124 :width: 70 % |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
2125 |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
2126 _________________ |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
2127 |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
2128 | For more information about pyGenomeTracks please consider our documentation on github_ |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
2129 |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
2130 .. _github: https://github.com/deeptools/pyGenomeTracks |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
2131 .. _`Nothjunge et al. (2017)`: https://www.nature.com/articles/s41467-017-01724-9 |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
2132 ]]></help> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
2133 <expand macro="citations" /> |
|
2074627b0f83
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit a68062b7e444233416bd30404be9bf92b6f1a363
iuc
parents:
diff
changeset
|
2134 </tool> |