Mercurial > repos > artbio > small_rna_maps
annotate small_rna_maps.xml @ 6:a3be3601bcb3 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 9f9c64aff0d225881bedb97bd5035ccbca945d9d
author | artbio |
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date | Mon, 09 Oct 2017 11:07:09 -0400 |
parents | 12c14642e6ac |
children | a96e6a7df2b7 |
rev | line source |
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6
a3be3601bcb3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 9f9c64aff0d225881bedb97bd5035ccbca945d9d
artbio
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changeset
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1 <tool id="small_rna_maps" name="small_rna_maps" version="2.1.0"> |
0
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
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2 <description></description> |
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
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changeset
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3 <requirements> |
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff
changeset
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4 <requirement type="package" version="1.11.2=py27_0">numpy</requirement> |
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff
changeset
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5 <requirement type="package" version="0.11.2.1=py27_0">pysam</requirement> |
5
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
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changeset
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6 <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
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changeset
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7 <requirement type="package" version="0.6_28=r3.3.2_0">r-latticeextra</requirement> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
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diff
changeset
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8 <requirement type="package" version="2.2.1=r3.3.2_0">r-gridextra</requirement> |
0
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff
changeset
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9 </requirements> |
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
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changeset
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10 <stdio> |
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
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11 <exit_code range="1:" level="fatal" description="Tool exception" /> |
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
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changeset
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12 </stdio> |
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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changeset
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13 <command detect_errors="exit_code"><![CDATA[ |
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507383cce5a8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
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14 #for $file in $inputs |
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6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
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changeset
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15 samtools index '$file' && |
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
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changeset
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16 #end for |
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
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17 python '$__tool_directory__'/small_rna_maps.py |
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507383cce5a8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
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18 --inputs |
507383cce5a8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
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changeset
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19 #for $file in $inputs |
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6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff
changeset
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20 '$file' |
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff
changeset
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21 #end for |
2
507383cce5a8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
parents:
1
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changeset
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22 --sample_names |
507383cce5a8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
parents:
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changeset
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23 #for $sample in $inputs |
0
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff
changeset
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24 '$sample.name' |
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff
changeset
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25 #end for |
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12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
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diff
changeset
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26 #if str($plots_options.plots_options_selector ) == "two_plot": |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
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27 --plot_methods '${plots_options.first_plot}' '${plots_options.extra_plot}' |
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ed8b0142538d
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
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28 --outputs '$output_tab' '$extra_output_tab' && |
5
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
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29 #else: |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
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30 --plot_methods '${plots_options.first_plot}' |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
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31 --outputs '$output_tab' && |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
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32 #end if |
2
507383cce5a8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
parents:
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33 Rscript '$__tool_directory__'/small_rna_maps.r |
507383cce5a8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
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34 --first_dataframe '$output_tab' |
507383cce5a8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
parents:
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35 --extra_dataframe '$extra_output_tab' |
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a3be3601bcb3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 9f9c64aff0d225881bedb97bd5035ccbca945d9d
artbio
parents:
5
diff
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36 --normalization '$normalization' |
5
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
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diff
changeset
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37 #if str($plots_options.plots_options_selector ) == "two_plot": |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
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diff
changeset
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38 --first_plot_method '${plots_options.first_plot}' |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
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changeset
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39 --extra_plot_method '${plots_options.extra_plot}' |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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changeset
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40 #else: |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
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diff
changeset
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41 --first_plot_method '${plots_options.first_plot}' |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
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diff
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42 --extra_plot_method '' |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
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43 #end if |
2
507383cce5a8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
parents:
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44 --output_pdf '$output_pdf' |
0
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
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45 ]]></command> |
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff
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46 <inputs> |
5
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
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diff
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47 <param name="inputs" type="data" format="bam" label="Select multiple alignments to parse" multiple="True"/> |
6
a3be3601bcb3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 9f9c64aff0d225881bedb97bd5035ccbca945d9d
artbio
parents:
5
diff
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48 <param name="normalization" type="text" label="Enter size/normalization factors as a space-separated list. Leave blank for no normalization (default)" |
a3be3601bcb3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 9f9c64aff0d225881bedb97bd5035ccbca945d9d
artbio
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49 help="e.g. '1 0.75 1.23'. Values of the list map to the above selected files from bottom to top" /> |
5
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
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50 <conditional name="plots_options"> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
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51 <param name="plots_options_selector" type="select" label="Number of plots per chromosome"> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
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52 <option value="one_plot">Just one plot per chromosome</option> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
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53 <option value="two_plot" selected="True">Two plots per chromosome</option> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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54 </param> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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55 <when value="two_plot"> |
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a3be3601bcb3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 9f9c64aff0d225881bedb97bd5035ccbca945d9d
artbio
parents:
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diff
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56 <param name="first_plot" type="select" label="Select the type of the first plot"> |
5
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
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57 <option value="Counts">Counts</option> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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58 <option value="Coverage">Coverage</option> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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59 <option value="Mean">Mean Sizes</option> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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60 <option value="Median">Median Sizes</option> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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61 <option value="Size">Size Distributions</option> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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62 </param> |
6
a3be3601bcb3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 9f9c64aff0d225881bedb97bd5035ccbca945d9d
artbio
parents:
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diff
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63 <param name="extra_plot" type="select" label="Select the type of the second plot"> |
5
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
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64 <option value="Counts">Counts</option> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
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65 <option value="Coverage">Coverage</option> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
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diff
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66 <option value="Mean">Mean Sizes</option> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
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diff
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67 <option value="Median">Median Sizes</option> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
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68 <option value="Size">Size Distributions</option> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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69 </param> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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70 </when> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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71 <when value="one_plot"> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
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72 <param name="first_plot" type="select" label="select the type of the first plot"> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
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diff
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73 <option value="Counts">Counts</option> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
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diff
changeset
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74 <option value="Coverage">Coverage</option> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
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75 <option value="Mean">Mean Sizes</option> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
76 <option value="Median">Median Sizes</option> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
77 <option value="Size">Size Distributions</option> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
78 </param> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
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diff
changeset
|
79 </when> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
80 </conditional> |
0
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff
changeset
|
81 </inputs> |
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff
changeset
|
82 |
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff
changeset
|
83 <outputs> |
2
507383cce5a8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
parents:
1
diff
changeset
|
84 <data format="tabular" name="output_tab" label="Read Count dataframe" /> |
5
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
85 <data format="tabular" name="extra_output_tab" label="$plots_options.extra_plot dataframe"> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
86 <filter>plots_options['plots_options_selector'] == 'two_plot'</filter> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
87 </data> |
0
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff
changeset
|
88 <data format="pdf" name="output_pdf" label="PDF file" /> |
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff
changeset
|
89 |
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff
changeset
|
90 </outputs> |
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff
changeset
|
91 |
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff
changeset
|
92 <tests> |
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff
changeset
|
93 <test> |
2
507383cce5a8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
parents:
1
diff
changeset
|
94 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> |
5
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
95 <param name="plots_options_selector" value="two_plot" /> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
96 <param name="first_plot" value="Counts" /> |
0
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff
changeset
|
97 <param name="extra_plot" value="Mean" /> |
6
a3be3601bcb3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 9f9c64aff0d225881bedb97bd5035ccbca945d9d
artbio
parents:
5
diff
changeset
|
98 <param name="normalization" value="1 1" /> |
5
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
99 <output file="count.tab" name="output_tab" /> |
2
507383cce5a8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
parents:
1
diff
changeset
|
100 <output file="mean.tab" name="extra_output_tab" /> |
5
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
101 <output file="count-mean.pdf" name="output_pdf" /> |
0
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
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changeset
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102 </test> |
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff
changeset
|
103 <test> |
2
507383cce5a8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
parents:
1
diff
changeset
|
104 <param name="inputs" value="input1.bam,input1.bam" ftype="bam"/> |
5
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
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diff
changeset
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105 <param name="plots_options_selector" value="two_plot" /> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
106 <param name="first_plot" value="Counts" /> |
0
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
parents:
diff
changeset
|
107 <param name="extra_plot" value="Mean" /> |
6
a3be3601bcb3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 9f9c64aff0d225881bedb97bd5035ccbca945d9d
artbio
parents:
5
diff
changeset
|
108 <param name="normalization" value="1 1" /> |
5
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
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109 <output file="doubled_count.tab" name="output_tab" /> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
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110 <output file="doubled_mean.tab" name="extra_output_tab" /> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
111 <output file="doubled_count-mean.pdf" name="output_pdf" /> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
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diff
changeset
|
112 </test> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
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changeset
|
113 <test> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
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114 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
115 <param name="plots_options_selector" value="two_plot" /> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
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diff
changeset
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116 <param name="first_plot" value="Counts" /> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
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changeset
|
117 <param name="extra_plot" value="Median" /> |
6
a3be3601bcb3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 9f9c64aff0d225881bedb97bd5035ccbca945d9d
artbio
parents:
5
diff
changeset
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118 <param name="normalization" value="1 1" /> |
5
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
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changeset
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119 <output file="count.tab" name="output_tab" /> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
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diff
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|
120 <output file="median.tab" name="extra_output_tab" /> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
|
121 <output file="count-median.pdf" name="output_pdf" /> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
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changeset
|
122 </test> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
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diff
changeset
|
123 <test> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
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124 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
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diff
changeset
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125 <param name="plots_options_selector" value="two_plot" /> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
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diff
changeset
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126 <param name="first_plot" value="Counts" /> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
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127 <param name="extra_plot" value="Coverage" /> |
6
a3be3601bcb3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 9f9c64aff0d225881bedb97bd5035ccbca945d9d
artbio
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5
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128 <param name="normalization" value="1 1" /> |
5
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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129 <output file="count.tab" name="output_tab" /> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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130 <output file="coverage.tab" name="extra_output_tab" /> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
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131 <output file="count-coverage.pdf" name="output_pdf" /> |
0
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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changeset
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132 </test> |
6d48150495e3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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changeset
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133 <test> |
2
507383cce5a8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
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1
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134 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> |
5
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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135 <param name="plots_options_selector" value="two_plot" /> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
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changeset
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136 <param name="first_plot" value="Counts" /> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
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changeset
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137 <param name="extra_plot" value="Size" /> |
6
a3be3601bcb3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 9f9c64aff0d225881bedb97bd5035ccbca945d9d
artbio
parents:
5
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138 <param name="normalization" value="1 1" /> |
5
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
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139 <output file="count.tab" name="output_tab" /> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
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140 <output file="size.tab" name="extra_output_tab" /> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
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changeset
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141 <output file="count-size.pdf" name="output_pdf" /> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
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142 </test> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
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diff
changeset
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143 <test> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
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144 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
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145 <param name="plots_options_selector" value="two_plot" /> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
diff
changeset
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146 <param name="first_plot" value="Size" /> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
4
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changeset
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147 <param name="extra_plot" value="Counts" /> |
6
a3be3601bcb3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 9f9c64aff0d225881bedb97bd5035ccbca945d9d
artbio
parents:
5
diff
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148 <param name="normalization" value="1 1" /> |
5
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
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changeset
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149 <output file="size.tab" name="output_tab" /> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
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changeset
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150 <output file="count.tab" name="extra_output_tab" /> |
12c14642e6ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents:
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151 <output file="size-count.pdf" name="output_pdf" /> |
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152 </test> |
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153 <test> |
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154 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> |
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155 <param name="plots_options_selector" value="two_plot" /> |
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156 <param name="first_plot" value="Size" /> |
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157 <param name="extra_plot" value="Counts" /> |
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158 <param name="normalization" value="1 0.75" /> |
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159 <output file="size.tab" name="output_tab" /> |
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160 <output file="count.tab" name="extra_output_tab" /> |
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161 <output file="size-count_normed.pdf" name="output_pdf" /> |
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162 </test> |
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163 <test> |
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164 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> |
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165 <param name="plots_options_selector" value="one_plot" /> |
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166 <param name="normalization" value="1 1" /> |
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167 <param name="first_plot" value="Counts" /> |
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168 <output file="count.tab" name="output_tab" /> |
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169 <output file="count.pdf" name="output_pdf" /> |
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170 </test> |
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171 <test> |
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172 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> |
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173 <param name="plots_options_selector" value="one_plot" /> |
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174 <param name="first_plot" value="Size" /> |
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175 <param name="normalization" value="1 1" /> |
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176 <output file="size.tab" name="output_tab" /> |
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177 <output file="size.pdf" name="output_pdf" /> |
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178 </test> |
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179 <test> |
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180 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> |
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181 <param name="plots_options_selector" value="one_plot" /> |
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182 <param name="first_plot" value="Coverage" /> |
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183 <param name="normalization" value="1 1" /> |
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184 <output file="coverage.tab" name="output_tab" /> |
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185 <output file="coverage.pdf" name="output_pdf" /> |
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186 </test> |
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187 <test> |
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188 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> |
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189 <param name="plots_options_selector" value="one_plot" /> |
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190 <param name="first_plot" value="Coverage" /> |
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191 <param name="normalization" value="1 0.2" /> |
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192 <output file="coverage.tab" name="output_tab" /> |
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193 <output file="coverage_normed.pdf" name="output_pdf" /> |
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194 </test> |
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195 </tests> |
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196 |
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197 |
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198 <help> |
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199 |
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200 **What it does** |
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201 |
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202 Plots maps of (1) read counts, (2) mean sizes, (3) median sizes, (4) coverage depth or (5) |
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203 size read distribution along chromosome references. |
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204 |
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205 Mean sizes and median sizes are the mean and the median sizes, respectively, of all reads |
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206 whose 5' end map to a given coordinate in a chromosome reference. |
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207 Coverage depths are computed from the input bam alignment files using the python pysam module. |
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208 |
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209 The variables mentioned above (1-5) can be plotted either separately or in all possible |
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210 pairwise combinations. |
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211 |
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212 For comparison purpose, values from bam alignment files can be normalized by a size factor |
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213 before plotting. If the normalization field is leaved blank, default normalization of 1 |
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214 is assumed. |
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215 |
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216 **Inputs** |
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217 |
2
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218 bam alignment files that must be |
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219 |
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220 - single-read |
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221 - sorted |
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222 - mapping to the same reference |
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223 |
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224 Optionally, a space-separated list of normalization/size factors may be added before plotting. |
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225 This list maps to the selected bam alignments from bottom to top. |
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226 |
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227 **Output** |
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228 |
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229 A pdf file generated by the R package lattice |
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230 |
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231 One or two dataframes used to plot data |
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232 |
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233 </help> |
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234 |
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235 <citations> |
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236 <citation type="doi">10.1093/bioinformatics/btp352</citation> |
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237 <citation type="bibtex">@Book{, |
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238 title = {Lattice: Multivariate Data Visualization with R}, |
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239 author = {Deepayan Sarkar}, |
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240 publisher = {Springer}, |
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241 address = {New York}, |
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242 year = {2008}, |
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243 note = {ISBN 978-0-387-75968-5}, |
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244 url = {http://lmdvr.r-forge.r-project.org}, |
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245 }</citation> |
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246 </citations> |
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247 </tool> |
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248 |