Mercurial > repos > iuc > gffcompare
annotate gffcompare.xml @ 6:3c5e024a18cf draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit 8e8c67f4aa5ab37fc28c512b4e9e7f26a2d1e604
| author | iuc |
|---|---|
| date | Fri, 04 Oct 2024 08:47:42 +0000 |
| parents | f99dd58de04f |
| children |
| rev | line source |
|---|---|
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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changeset
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1 <tool id="gffcompare" name="GffCompare" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> |
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3c97c841a443
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
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2 <description>compare assembled transcripts to a reference annotation</description> |
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2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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3 <macros> |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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4 <import>macros.xml</import> |
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2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
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5 </macros> |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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changeset
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6 <xrefs> |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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changeset
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7 <xref type="bio.tools">gffcompare</xref> |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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changeset
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8 </xrefs> |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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changeset
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9 <expand macro="requirements" /> |
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3c97c841a443
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff
changeset
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10 <version_command>gffcompare -v | awk '{print $2}'</version_command> |
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f99d7825a501
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit a5352fb7f073b0083b750c5cf7d283ebcc16b30d
iuc
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11 <command detect_errors="aggressive"><![CDATA[ |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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12 #import re |
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2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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13 |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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changeset
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14 #set escaped_element_identifiers = [re.sub('[^\w\-]', '_', str(_.element_identifier)) for _ in $gffinputs] |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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changeset
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15 #for $input, $escaped_element_identifier in zip($gffinputs, $escaped_element_identifiers): |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
4
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changeset
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16 ln -s '$input' '$escaped_element_identifier' && |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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diff
changeset
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17 #end for |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
4
diff
changeset
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18 #if $conditional_annotation.selector == "yes": |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
4
diff
changeset
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19 #if $conditional_annotation.ref_source.selector == "history": |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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changeset
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20 ln -s '$conditional_annotation.ref_source.reference_annotation' reference_annotation && |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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changeset
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21 #else: |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
4
diff
changeset
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22 ln -s '${conditional_annotation.ref_source.index.fields.path}' reference_annotation && |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
4
diff
changeset
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23 #end if |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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diff
changeset
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24 #end if |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
4
diff
changeset
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25 #if $seq_data.selector == "Yes": |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
4
diff
changeset
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26 #if $seq_data.seq_source.index_source == "history": |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
4
diff
changeset
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27 ln -s '$seq_data.seq_source.ref_genome' ref_seq.fa && |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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changeset
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28 samtools faidx ref_seq.fa && |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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diff
changeset
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29 #else: |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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diff
changeset
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30 ln -s '${seq_data.seq_source.index.fields.path}' ref_seq.fa && |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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changeset
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31 #end if |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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changeset
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32 #end if |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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33 gffcompare -V |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
4
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changeset
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34 #if $conditional_annotation.selector == "yes": |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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35 -r reference_annotation |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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36 $conditional_annotation.R |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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37 $conditional_annotation.Q |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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changeset
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38 $conditional_annotation.conditional_strict.selector |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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39 #if $conditional_annotation.conditional_strict.selector == '--strict-match' |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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40 -e $conditional_annotation.conditional_strict.e |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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41 #end if |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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42 $conditional_annotation.discard_single_exon |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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43 $conditional_annotation.conditional_duplication.selector |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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44 #if $conditional_annotation.conditional_duplication.selector == "-D" |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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45 $conditional_annotation.conditional_duplication.S |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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46 #end if |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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47 $conditional_annotation.no_merge |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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48 #end if |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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49 $refmap_tmap |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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50 #if $seq_data.selector == "Yes": |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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51 -s ref_seq.fa |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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52 #end if |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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53 -d $max_dist_group |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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54 $chr_stats |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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55 -p '$adv_output.p' |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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56 $adv_output.A |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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57 $adv_output.C |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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58 $adv_output.X |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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59 $adv_output.K |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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60 #for $escaped_element_identifier in $escaped_element_identifiers: |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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61 '$escaped_element_identifier' |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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62 #end for |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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63 #if len($gffinputs) == 1 and $refmap_tmap == 'true' |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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64 && mv *tmap output.tmap |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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65 #if $seq_data.selector == "Yes" |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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66 && mv *refmap output.refmap |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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67 #end if |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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68 #end if |
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1
c80cdc2eac6d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit fc3616bd1463afef9681cd7c431ac29f79e37e74
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69 ]]></command> |
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3c97c841a443
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
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70 <inputs> |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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71 <param format="gtf,gff3" name="gffinputs" type="data" label="GTF inputs for comparison" help="" multiple="true" /> |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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72 <conditional name="conditional_annotation"> |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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73 <param name="selector" type="select" label="Use reference annotation"> |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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74 <option value="no">No</option> |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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75 <option value="yes">Yes</option> |
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3c97c841a443
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
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76 </param> |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
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77 <when value="yes"> |
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78 <conditional name="ref_source"> |
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79 <param label="Choose the source for the reference annotation" name="selector" type="select"> |
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80 <option value="cached">Locally cached</option> |
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81 <option value="history" selected="true">History</option> |
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82 </param> |
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83 <when value="cached"> |
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84 <param argument="-r" label="Using reference annotation" name="index" type="select"> |
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85 <options from_data_table="gene_sets"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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86 <filter column="dbkey" key="dbkey" ref="gffinputs" type="data_meta" /> |
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87 </options> |
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88 <validator message="No reference annotation is available for the build associated with the selected input dataset" type="no_options" /> |
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89 </param> |
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90 </when> |
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91 <when value="history"> |
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92 <param argument="-r" name="reference_annotation" type="data" format="gff3,gtf" label="Reference annotation" |
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93 help="Requires an annotation file in GFF3 or GTF format"/> |
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94 </when> |
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95 </conditional> |
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96 <param argument="-R" falsevalue="" truevalue="-R" type="boolean" label="Sn correction" help="Consider only the reference transcripts that |
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97 overlap any of the input transfrags"/> |
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98 <param argument="-Q" falsevalue="" truevalue="-Q" type="boolean" label="Sp correction" help="Consider only the input transcripts that overlap |
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99 any of the reference transcripts. Warning: this will discard all 'novel' loci!"/> |
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100 <conditional name="conditional_strict"> |
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101 <param name="selector" argument="--strict-match" type="select" label="Strict match" help="Make the accuracy estimation |
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102 at transcript level much more stringtent by only allowing a limited variation of the outer coordinates of the terminal exons. Transcript |
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103 matching takes into account the -e range for terminal exons; code '=' is only assigned if transcript ends are within that range, otherwiscode |
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104 '~' is assigned for intron chain match or single-exon"> |
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105 <option value="">No</option> |
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106 <option value="--strict-match">Yes</option> |
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107 </param> |
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108 <when value=""/> |
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109 <when value="--strict-match"> |
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110 <param argument="-e" label="Maximum range of variation for the free ends of terminal exons" type="integer" value="100" /> |
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111 </when> |
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112 </conditional> |
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113 <param name="discard_single_exon" argument="-M/-N" type="select" label="Discard single-exon transcripts" help="If -S and also --strict-match is given, |
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114 exact matching of all exon boundaries is required"> |
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115 <option value="" selected="true">No</option> |
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116 <option value="-M">Discard single-exon transfrags and reference transcripts</option> |
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117 <option value="-N">Discard single-exon reference transcripts</option> |
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118 </param> |
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119 <conditional name="conditional_duplication"> |
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120 <param name="selector" argument="-D" type="select" label="Discart duplicate query transfrags" help="Discard duplicate query transfrags (i.e. same |
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121 intron chain) within a single sample (disable annotation mode for a single file); this option is automatically enabled when multiple query files are provided"> |
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122 <option value="">No</option> |
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123 <option value="-D">Yes</option> |
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124 </param> |
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125 <when value=""/> |
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126 <when value="-D"> |
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127 <param argument="-S" type="boolean" truevalue="-S" falsevalue="" checked="false" label="Strict duplicate checking" help="When -D is enabled (or |
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128 multiple query files are provided), perform a more strict duplicate checking: only discard matching (same intron chain) query transcripts from |
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129 the same sample if their boundaries are fully contained within (or same with) matching transcripts if --strict-match is also given, exact match |
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130 of all exons is required" /> |
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131 </when> |
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132 </conditional> |
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133 <param argument="--no-merge" type="boolean" checked="false" truevalue="--no-merge" falsevalue="" label="Disable close-exon merging" |
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134 help="Default: merge exons separated by 'introns' shorter than 5 bases" /> |
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135 </when> |
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136 <when value="no"/> |
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137 </conditional> |
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138 <conditional name="seq_data"> |
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139 <param name="selector" type="select" label="Use sequence data" help="Use sequence data for some optional classification functions, including the addition of the p_id attribute required by Cuffdiff." > |
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140 <option value="no">No</option> |
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141 <option value="yes">Yes</option> |
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0
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142 </param> |
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143 <when value="no"/> |
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144 <when value="yes"> |
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0
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145 <conditional name="seq_source"> |
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146 <param label="Choose the source for the reference sequence" name="index_source" type="select"> |
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0
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147 <option value="cached">Locally cached</option> |
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148 <option value="history" selected="true">History</option> |
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0
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149 </param> |
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150 <when value="cached"> |
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151 <param argument="-s" label="Using reference genome" name="index" type="select"> |
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152 <options from_data_table="fasta_indexes"> |
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153 <filter column="dbkey" key="dbkey" ref="gffinputs" type="data_meta" /> |
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154 </options> |
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155 <validator message="No reference genome is available for the build associated with the selected input dataset" type="no_options" /> |
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156 </param> |
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157 </when> |
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158 <when value="history"> |
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159 <param argument="-s" name="ref_genome" type="data" format="fasta" label="Reference genome" help="Optional. Repeats must be soft-masked (lower case) in order to be able to classify |
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160 transfrags as repeats"/> |
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161 </when> |
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162 </conditional> |
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163 </when> |
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164 </conditional> |
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165 <param argument="-d" name="max_dist_group" type="integer" value="100" min="0" help="Maximum distance (range) for grouping transcript start sites. Default: 100" label="Max distance for transcript grouping" /> |
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166 <param argument="--chr-stats" type="boolean" checked="false" truevalue="--chr-stats" falsevalue="" label="Stats per reference contig/chromosome" help="Show summary and accuracy data separately for each reference sequence in the transcript accuracy data set" /> |
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167 <param argument="-T" name="refmap_tmap" type="boolean" truevalue="" falsevalue="-T" checked="true" label="Generate TMAP and RefMap files for each input" help="TMAP are tabular files that store the information regarding the best match for each prediction in the reference. |
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168 RefMap files are tabular files which store the information regarding the best match for each reference transcript, among all possible prediction models. More information in the help section"/> |
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169 <section name="adv_output" title="Combined GTF output parameters"> |
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170 <param argument="-p" type="text" value="TCONS" label="Name prefix for consensus transcripts"> |
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171 <sanitizer invalid_char=""> |
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172 <valid initial="string.letters,string.digits"> |
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173 <add value="_" /> |
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174 <add value="-" /> |
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175 </valid> |
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176 </sanitizer> |
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177 <validator type="regex">[0-9a-zA-Z_-]+</validator> |
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178 </param> |
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179 <param argument="-C" type="boolean" checked="false" truevalue="-C" falsevalue="" label="Discard matching and 'contained' transfrags" help="I.e. collapse intron-redundant transfrags across all query files" /> |
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180 <param argument="-A" type="boolean" checked="false" truevalue="-A" falsevalue="" label="Discard the 'contained' transfrags except intron-redundant transfrags starting with a different 5' exon" help="Like -C but does not discard intron-redundant transfrags if they start with a different 5' exon" /> |
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181 <param argument="-X" type="boolean" checked="false" truevalue="-X" falsevalue="" label="Discard the 'contained' transfrags also if ends stick out within the container's introns" help="Like -C but also discard contained transfrags if transfrag ends stick out within the container's introns" /> |
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182 <param argument="-K" type="boolean" checked="false" truevalue="-K" falsevalue="" label="Do NOT discard any redundant transfrag matching a reference" help="For -C/-A/-X" /> |
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183 </section> |
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184 </inputs> |
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185 <outputs> |
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186 <data name="transcripts_annotated" format="gtf" from_work_dir="gffcmp.annotated.gtf" label="${tool.name} on ${on_string}: annotated transcripts"> |
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187 <filter>conditional_annotation['selector'] == "yes"</filter> |
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188 <filter>len(gffinputs) == 1</filter> |
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189 </data> |
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190 <data name="transcripts_combined" format="gtf" from_work_dir="gffcmp.combined.gtf" label="${tool.name} on ${on_string}: combined transcripts" > |
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191 <filter>len(gffinputs) > 1</filter> |
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192 </data> |
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193 <collection name="refmap_output_collection" type="list" label="${tool.name} on ${on_string}: RefMap"> |
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194 <discover_datasets pattern="gffcmp\.(?P<designation>.+)\.refmap" ext="tabular" /> |
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195 <filter>conditional_annotation['selector'] == 'yes'</filter> |
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196 <filter>len(gffinputs) > 1</filter> |
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197 <filter>refmap_tmap</filter> |
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198 </collection> |
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199 <data name="refmap_output" format="tabular" from_work_dir="output.refmap" label="${tool.name} on ${on_string}: RefMap"> |
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200 <filter>conditional_annotation['selector'] == 'yes'</filter> |
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201 <filter>len(gffinputs) == 1</filter> |
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202 <filter>refmap_tmap</filter> |
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203 </data> |
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204 <collection name="tmap_output_collection" type="list" label="${tool.name} on ${on_string}: TMAP"> |
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205 <discover_datasets pattern="gffcmp\.(?P<designation>.+)\.tmap" ext="tabular" /> |
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206 <filter>refmap_tmap</filter> |
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207 <filter>len(gffinputs) > 1</filter> |
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208 </collection> |
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209 <data name="tmap_output" format="tabular" from_work_dir="output.tmap" label="${tool.name} on ${on_string}: TMAP"> |
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210 <filter>refmap_tmap</filter> |
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211 <filter>len(gffinputs) == 1</filter> |
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212 </data> |
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213 <data name="transcripts_stats" format="txt" from_work_dir="gffcmp.stats" label="${tool.name} on ${on_string}: accuracy stats" /> |
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214 <data name="transcripts_loci" format="tabular" from_work_dir="gffcmp.loci" label="${tool.name} on ${on_string}: loci file" /> |
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215 <data name="transcripts_tracking" format="tabular" from_work_dir="gffcmp.tracking" label="${tool.name} on ${on_string}: tracking file" /> |
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216 </outputs> |
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217 <tests> |
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218 <!-- Test 01: 2 inputs, no reference, default options --> |
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219 <test expect_num_outputs="5"> |
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220 <param ftype="gtf" name="gffinputs" value="gffcompare_in1.gtf,gffcompare_in2.gtf" /> |
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221 <conditional name="conditional_annotation"> |
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222 <param name="selector" value="no"/> |
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223 </conditional> |
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224 <conditional name="seq_data"> |
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225 <param name="selector" value="no" /> |
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226 </conditional> |
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227 <assert_command> |
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228 <not_has_text text="-R " /> |
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229 <not_has_text text="-Q " /> |
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230 <not_has_text text="--strict-match " /> |
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231 <not_has_text text="-T " /> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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232 <has_text_matching expression="^.*gffcompare((?!-s).)*$" /> <!-- since ln also has -s a more complicated regexp is needed here to check if -s is not set --> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
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233 <not_has_text text="-M " /> |
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234 <not_has_text text="-N " /> |
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235 <has_text text="-d 100 " /> |
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236 <not_has_text text="-D " /> |
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237 <not_has_text text="--no-merge " /> |
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238 <has_text text="-p 'TCONS' " /> |
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239 <not_has_text text="-C " /> |
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240 <not_has_text text="-A " /> |
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241 <not_has_text text="-X " /> |
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242 <not_has_text text="-K " /> |
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243 </assert_command> |
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244 <output file="gffcompare_out1.stats" name="transcripts_stats" /> |
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245 <output file="gffcompare_out1.loci" name="transcripts_loci" /> |
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246 <output file="gffcompare_out1.tracking" name="transcripts_tracking" /> |
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247 <output file="gffcompare_out1.gtf" name="transcripts_combined" /> |
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248 <output_collection name="tmap_output_collection" type="list" count="2"/> |
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249 </test> |
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250 <!-- Test 02: 2 inputs, no reference, with refsequence, default options (but disable tmap output) --> |
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251 <test expect_num_outputs="4"> |
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252 <param ftype="gtf" name="gffinputs" value="gffcompare_in1.gtf,gffcompare_in2.gtf" /> |
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253 <param name="refmap_tmap" value="false"/> |
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254 <conditional name="conditional_annotation"> |
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255 <param name="selector" value="no"/> |
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256 </conditional> |
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257 <conditional name="seq_data"> |
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258 <param name="selector" value="Yes" /> |
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259 <conditional name="seq_source"> |
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260 <param name="index_source" value="history"/> |
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261 <param name="ref_file" ftype="fasta" value="sequence.fa"/> |
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262 </conditional> |
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263 </conditional> |
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264 <assert_command> |
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265 <not_has_text text="-R " /> |
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266 <not_has_text text="-Q " /> |
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267 <has_text text="-T " /> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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268 <has_text_matching expression="gffcompare.*-s " /> <!-- since ln also has -s a more complicated regexp is needed here to check if -s is set --> |
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269 <not_has_text text="-M " /> |
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270 <not_has_text text="-N " /> |
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271 <has_text text="-d 100 " /> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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272 <has_text text="-p 'TCONS' " /> |
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273 <not_has_text text="-C " /> |
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274 <not_has_text text="-A " /> |
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275 <not_has_text text="-X " /> |
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276 <not_has_text text="-K " /> |
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277 </assert_command> |
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278 <output file="gffcompare_out1.stats" name="transcripts_stats" compare="sim_size" /> |
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279 <output file="gffcompare_out1.loci" name="transcripts_loci" compare="sim_size" /> |
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280 <output file="gffcompare_out1.tracking" name="transcripts_tracking" compare="sim_size" /> |
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281 <output file="gffcompare_out1.gtf" name="transcripts_combined" compare="sim_size" /> |
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282 </test> |
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283 <!-- Test 03: 2 inputs, no reference, with cached refsequence, default options (but disable tmap output) --> |
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284 <test expect_num_outputs="4"> |
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285 <param ftype="gtf" name="gffinputs" value="gffcompare_in1.gtf,gffcompare_in2.gtf" dbkey="hg17" /> |
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286 <param name="refmap_tmap" value="false"/> |
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287 <conditional name="conditional_annotation"> |
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288 <param name="selector" value="no"/> |
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289 </conditional> |
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290 <conditional name="seq_data"> |
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291 <param name="selector" value="yes" /> |
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292 <conditional name="seq_source"> |
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293 <param name="index_source" value="cached"/> |
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294 <param name="index" value="test_buildid"/> |
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295 </conditional> |
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296 </conditional> |
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297 <assert_command> |
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298 <not_has_text text="-R " /> |
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299 <not_has_text text="-Q " /> |
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300 <has_text text="-T " /> |
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iuc
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301 <has_text_matching expression="gffcompare.*-s " /> |
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3
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iuc
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302 <not_has_text text="-M " /> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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changeset
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303 <not_has_text text="-N " /> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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304 <has_text text="-d 100 " /> |
|
4
0f710191a66d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
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changeset
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305 <has_text text="-p 'TCONS' " /> |
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3
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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changeset
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306 <not_has_text text="-C " /> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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changeset
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307 <not_has_text text="-A " /> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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changeset
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308 <not_has_text text="-X " /> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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changeset
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309 <not_has_text text="-K " /> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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310 </assert_command> |
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6
3c5e024a18cf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit 8e8c67f4aa5ab37fc28c512b4e9e7f26a2d1e604
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311 <output file="gffcompare_out1.stats" name="transcripts_stats" compare="sim_size" /> |
|
3
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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changeset
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312 <output file="gffcompare_out1.loci" name="transcripts_loci" compare="sim_size" /> |
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2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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changeset
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313 <output file="gffcompare_out1.tracking" name="transcripts_tracking" compare="sim_size" /> |
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2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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changeset
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314 <output file="gffcompare_out1.gtf" name="transcripts_combined" compare="sim_size" /> |
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2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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changeset
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315 </test> |
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5
f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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316 <!-- Test 04: 2 inputs and reference, default options --> |
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1
c80cdc2eac6d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
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317 <test expect_num_outputs="6"> |
|
c80cdc2eac6d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit fc3616bd1463afef9681cd7c431ac29f79e37e74
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318 <param ftype="gtf" name="gffinputs" value="gffcompare_in1.gtf,gffcompare_in2.gtf" /> |
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5
f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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319 <conditional name="conditional_annotation"> |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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320 <param name="selector" value="yes"/> |
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3
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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changeset
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321 <conditional name="ref_source"> |
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2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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changeset
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322 <param name="ref_source_sel" value="history"/> |
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2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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changeset
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323 <param ftype="gtf" name="reference_annotation" value="gffcompare_in3.gtf" /> |
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2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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324 </conditional> |
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5
f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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changeset
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325 <conditional name="conditional_strict"> |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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326 <param name="selector" value="--strict-match"/> |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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327 <param name="e" value="100"/> |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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328 </conditional> |
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3
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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329 </conditional> |
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2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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330 <conditional name="seq_data"> |
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5
f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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331 <param name="seletor" value="no" /> |
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1
c80cdc2eac6d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
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332 </conditional> |
|
3
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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changeset
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333 <assert_command> |
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2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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changeset
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334 <not_has_text text="-R " /> |
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2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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changeset
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335 <not_has_text text="-Q " /> |
|
5
f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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336 <has_text text="--strict-match " /> |
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3
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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changeset
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337 <not_has_text text="-T " /> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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changeset
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338 <not_has_text text="-M " /> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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changeset
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339 <not_has_text text="-N " /> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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changeset
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340 <has_text text="-e 100 " /> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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changeset
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341 <has_text text="-d 100 " /> |
|
4
0f710191a66d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
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342 <not_has_text text="-D " /> |
|
0f710191a66d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
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343 <not_has_text text="--no-merge " /> |
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0f710191a66d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
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344 <not_has_text text="--chr-stats" /> |
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0f710191a66d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
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345 <has_text text="-p 'TCONS' " /> |
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3
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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changeset
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346 <not_has_text text="-C " /> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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changeset
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347 <not_has_text text="-A " /> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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changeset
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348 <not_has_text text="-X " /> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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changeset
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349 <not_has_text text="-K " /> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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350 </assert_command> |
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5
f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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diff
changeset
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351 <output file="gffcompare_out2.stats" name="transcripts_stats" compare="sim_size" /> |
|
4
0f710191a66d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
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352 <output file="gffcompare_out2.loci" name="transcripts_loci" compare="sim_size" /> |
|
3
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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changeset
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353 <output file="gffcompare_out2.tracking" name="transcripts_tracking" /> |
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2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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changeset
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354 <output file="gffcompare_out2.gtf" name="transcripts_combined" /> |
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5
f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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changeset
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355 <output_collection name="refmap_output_collection" type="list" count="2"> |
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3
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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changeset
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356 <element name="gffcompare_in1_gtf" file="gffcompare_out2-1.refmap" ftype="tabular" /> |
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2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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changeset
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357 <element name="gffcompare_in2_gtf" file="gffcompare_out2-2.refmap" ftype="tabular" /> |
|
1
c80cdc2eac6d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
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358 </output_collection> |
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5
f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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changeset
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359 <output_collection name="tmap_output_collection" type="list" count="2"> |
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3
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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changeset
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360 <element name="gffcompare_in1_gtf" file="gffcompare_out2-1.tmap" ftype="tabular" /> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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changeset
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361 <element name="gffcompare_in2_gtf" file="gffcompare_out2-2.tmap" ftype="tabular" /> |
|
1
c80cdc2eac6d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
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diff
changeset
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362 </output_collection> |
|
0
3c97c841a443
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
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diff
changeset
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363 </test> |
|
5
f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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364 <!-- Test 05: 2 inputs and reference (cached), non default options --> |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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diff
changeset
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365 <test expect_num_outputs="6"> |
|
3
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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366 <param ftype="gtf" name="gffinputs" value="gffcompare_in1.gtf,gffcompare_in2.gtf" dbkey="hg17" /> |
|
5
f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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diff
changeset
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367 <conditional name="conditional_annotation"> |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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368 <param name="selector" value="yes"/> |
|
3
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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diff
changeset
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369 <conditional name="ref_source"> |
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2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
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370 <param name="ref_source_sel" value="cached"/> |
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2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
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371 <param name="index" value="test_buildid"/> |
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2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
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372 </conditional> |
|
5
f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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diff
changeset
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373 <param name="R" value="true"/> |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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diff
changeset
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374 <param name="Q" value="true"/> |
|
f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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changeset
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375 <param name="discard_single_exon" value="-M"/> |
|
f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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diff
changeset
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376 <param name="no_merge" value="true"/> |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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diff
changeset
|
377 <conditional name="conditional_strict"> |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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diff
changeset
|
378 <param name="selector" value="--strict-match"/> |
|
f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
4
diff
changeset
|
379 <param name="e" value="101"/> |
|
f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
4
diff
changeset
|
380 </conditional> |
|
f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
4
diff
changeset
|
381 <conditional name="conditional_duplication"> |
|
f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
4
diff
changeset
|
382 <param name="selector" value="-D"/> |
|
f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
4
diff
changeset
|
383 <param name="S" value="false"/> |
|
f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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diff
changeset
|
384 </conditional> |
|
3
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
385 </conditional> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
386 <param name="max_dist_group" value="99" /> |
|
5
f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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diff
changeset
|
387 <param name="chr_stats" value="true" /> |
|
3
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
388 <assert_command> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
389 <has_text text="-R " /> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
390 <has_text text="-Q " /> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
391 <has_text text="--strict-match " /> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
392 <not_has_text text="-T " /> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
393 <has_text text="-M " /> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
394 <not_has_text text="-N " /> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
2
diff
changeset
|
395 <has_text text="-e 101 " /> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
396 <has_text text="-d 99 " /> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
397 <has_text text="-D " /> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
398 <has_text text="--no-merge " /> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
399 <has_text text="--chr-stats" /> |
|
4
0f710191a66d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
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diff
changeset
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400 <has_text text="-p 'TCONS' " /> |
|
3
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
401 <not_has_text text="-C " /> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
402 <not_has_text text="-A " /> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
403 <not_has_text text="-X " /> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
404 <not_has_text text="-K " /> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
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405 </assert_command> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
406 <output file="gffcompare_out2.stats" name="transcripts_stats" compare="sim_size" /> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
407 <output file="gffcompare_out2.loci" name="transcripts_loci" compare="sim_size" /> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
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408 <output file="gffcompare_out2.tracking" name="transcripts_tracking" compare="sim_size" /> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
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409 <output file="gffcompare_out2.gtf" name="transcripts_combined" compare="sim_size" delta="50000"/> |
|
5
f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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diff
changeset
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410 <output_collection name="refmap_output_collection" type="list" count="0"/> <!-- because of -M no refmaps are created --> |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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diff
changeset
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411 <output_collection name="tmap_output_collection" type="list" count="2"/> |
|
3
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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changeset
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412 </test> |
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5
f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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diff
changeset
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413 <!-- Test 06: 2 inputs and reference, non default advanced options --> |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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diff
changeset
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414 <test expect_num_outputs="6"> |
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3
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
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415 <param ftype="gtf" name="gffinputs" value="gffcompare_in1.gtf,gffcompare_in2.gtf" /> |
|
5
f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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diff
changeset
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416 <conditional name="conditional_annotation"> |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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diff
changeset
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417 <param name="selector" value="yes"/> |
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3
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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diff
changeset
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418 <conditional name="ref_source"> |
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2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
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419 <param name="ref_source_sel" value="history"/> |
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2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
420 <param ftype="gtf" name="reference_annotation" value="gffcompare_in3.gtf" /> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
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421 </conditional> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
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422 </conditional> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
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423 <conditional name="seq_data"> |
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5
f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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diff
changeset
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424 <param name="selector" value="no" /> |
|
3
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
425 </conditional> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
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426 <section name="adv_output"> |
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2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
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427 <param name="p" value="OTHER" /> |
|
5
f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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diff
changeset
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428 <param name="C" value="true" /> |
|
f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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diff
changeset
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429 <param name="A" value="true" /> |
|
f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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diff
changeset
|
430 <param name="X" value="true" /> |
|
f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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diff
changeset
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431 <param name="K" value="true" /> |
|
3
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
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432 </section> |
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2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
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433 <assert_command> |
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2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
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434 <not_has_text text="-R " /> |
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2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
435 <not_has_text text="-Q " /> |
|
4
0f710191a66d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
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diff
changeset
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436 <not_has_text text="--strict-match " /> |
|
3
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
437 <not_has_text text="-T " /> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
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438 <not_has_text text="-M " /> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
439 <not_has_text text="-N " /> |
|
5
f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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diff
changeset
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440 <not_has_text text="-e 100 " /> |
|
3
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
441 <has_text text="-d 100 " /> |
|
4
0f710191a66d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
3
diff
changeset
|
442 <not_has_text text="-D " /> |
|
0f710191a66d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
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diff
changeset
|
443 <not_has_text text="--no-merge " /> |
|
0f710191a66d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
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diff
changeset
|
444 <not_has_text text="--chr-stats" /> |
|
0f710191a66d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
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diff
changeset
|
445 <has_text text="-p 'OTHER' " /> |
|
3
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
446 <has_text text="-C " /> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
447 <has_text text="-A " /> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
448 <has_text text="-X " /> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
449 <has_text text="-K " /> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
2
diff
changeset
|
450 </assert_command> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
2
diff
changeset
|
451 <output file="gffcompare_out2.stats" name="transcripts_stats" compare="sim_size" /> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
2
diff
changeset
|
452 <output file="gffcompare_out2.loci" name="transcripts_loci" compare="sim_size" /> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
2
diff
changeset
|
453 <output file="gffcompare_out2.tracking" name="transcripts_tracking" compare="sim_size" /> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
2
diff
changeset
|
454 <output file="gffcompare_out2.gtf" name="transcripts_combined" compare="sim_size" delta="50000"/> |
|
5
f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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changeset
|
455 <output_collection name="tmap_output_collection" type="list" count="2"/> |
|
f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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changeset
|
456 <output_collection name="tmap_output_collection" type="list" count="2"/> |
|
3
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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diff
changeset
|
457 </test> |
|
5
f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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diff
changeset
|
458 <!-- Test 07: 2 inputs and reference, default options, no tmap or refmap output --> |
|
3
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
459 <test expect_num_outputs="4"> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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changeset
|
460 <param ftype="gtf" name="gffinputs" value="gffcompare_in1.gtf,gffcompare_in2.gtf" /> |
|
5
f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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diff
changeset
|
461 <param name="refmap_tmap" value="false"/> |
|
f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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diff
changeset
|
462 <conditional name="conditional_annotation"> |
|
f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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diff
changeset
|
463 <param name="selector" value="yes"/> |
|
3
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
464 <conditional name="ref_source"> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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changeset
|
465 <param name="ref_source_sel" value="history"/> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
466 <param ftype="gtf" name="reference_annotation" value="gffcompare_in3.gtf" /> |
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2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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changeset
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467 </conditional> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
468 </conditional> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
469 <conditional name="seq_data"> |
|
5
f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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changeset
|
470 <param name="selector" value="No" /> |
|
3
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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changeset
|
471 </conditional> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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changeset
|
472 <assert_command> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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changeset
|
473 <not_has_text text="-R " /> |
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2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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changeset
|
474 <not_has_text text="-Q " /> |
|
4
0f710191a66d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
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diff
changeset
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475 <not_has_text text="--strict-match " /> |
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3
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
476 <has_text text="-T " /> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
477 <not_has_text text="-M " /> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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changeset
|
478 <not_has_text text="-N " /> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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changeset
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479 <has_text text="-d 100 " /> |
|
4
0f710191a66d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
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changeset
|
480 <not_has_text text="-D " /> |
|
0f710191a66d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
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changeset
|
481 <not_has_text text="--no-merge " /> |
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0f710191a66d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
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changeset
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482 <not_has_text text="--chr-stats" /> |
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0f710191a66d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
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changeset
|
483 <has_text text="-p 'TCONS' " /> |
|
3
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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diff
changeset
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484 <not_has_text text="-C " /> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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diff
changeset
|
485 <not_has_text text="-A " /> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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changeset
|
486 <not_has_text text="-X " /> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
487 <not_has_text text="-K " /> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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changeset
|
488 </assert_command> |
|
4
0f710191a66d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
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diff
changeset
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489 <output file="gffcompare_out2.stats" name="transcripts_stats" lines_diff="2" /> |
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0f710191a66d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
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diff
changeset
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490 <output file="gffcompare_out2.loci" name="transcripts_loci" compare="sim_size" /> |
|
3
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
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491 <output file="gffcompare_out2.tracking" name="transcripts_tracking" /> |
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2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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diff
changeset
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492 <output file="gffcompare_out2.gtf" name="transcripts_combined" /> |
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2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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changeset
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493 </test> |
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5
f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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diff
changeset
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494 <!-- Test 08: 1 inputs and reference, default options, no tmap or refmap output --> |
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1
c80cdc2eac6d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
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diff
changeset
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495 <test expect_num_outputs="4"> |
|
c80cdc2eac6d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
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diff
changeset
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496 <param ftype="gtf" name="gffinputs" value="gffcompare_in4.gtf" /> |
|
5
f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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changeset
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497 <param name="refmap_tmap" value="false"/> |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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changeset
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498 <conditional name="conditional_annotation"> |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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changeset
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499 <param name="selector" value="yes"/> |
|
3
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
500 <conditional name="ref_source"> |
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2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
501 <param name="ref_source_sel" value="history"/> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
502 <param ftype="gtf" name="reference_annotation" value="gffcompare_in5.gtf" /> |
|
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
503 </conditional> |
|
5
f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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changeset
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504 <param name="R" value="true"/> |
|
f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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diff
changeset
|
505 <param name="Q" value="false"/> |
|
f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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diff
changeset
|
506 <conditional name="conditional_strict"> |
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f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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changeset
|
507 <param name="selector" value="--strict-match"/> |
|
f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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changeset
|
508 <param name="e" value="100"/> |
|
f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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diff
changeset
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509 </conditional> |
|
f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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diff
changeset
|
510 <param name="discard_single_exon" value=""/> |
|
1
c80cdc2eac6d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
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0
diff
changeset
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511 </conditional> |
|
0
3c97c841a443
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
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diff
changeset
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512 <param name="max_dist_group" value="100" /> |
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4
0f710191a66d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents:
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diff
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513 <output file="gffcompare_out3.stats" name="transcripts_stats"/> |
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0f710191a66d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
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diff
changeset
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514 <output file="gffcompare_out3.loci" name="transcripts_loci" compare="sim_size" /> |
|
3
2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
515 <output file="gffcompare_out3.tracking" name="transcripts_tracking" /> |
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2bb86e2c417f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
516 <output file="gffcompare_out3.gtf" name="transcripts_annotated" /> |
|
0
3c97c841a443
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
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diff
changeset
|
517 </test> |
|
3c97c841a443
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
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diff
changeset
|
518 </tests> |
|
3c97c841a443
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff
changeset
|
519 <help> |
|
3c97c841a443
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
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changeset
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520 <![CDATA[ |
|
5
f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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diff
changeset
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521 |
|
f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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changeset
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522 .. class:: infomark |
|
f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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diff
changeset
|
523 |
|
0
3c97c841a443
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff
changeset
|
524 **GffCompare Overview** |
|
3c97c841a443
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
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diff
changeset
|
525 |
|
5
f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
4
diff
changeset
|
526 GffCompare is designed to systematically compare one or more sets of transcript predictions to a reference annotation at different levels of granularity (base level, exon level, |
|
f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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diff
changeset
|
527 transcript level etc.), and in the process to provide a way to "annotate" such transcript predictions based on their overlaps or proximity to reference annotation transcripts. |
|
f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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diff
changeset
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528 When multiple transcript files (samples) are provided, GffCompare generates a non-redundant combined set of transcripts, tracking structurally equivalent transcripts across multiple |
|
f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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diff
changeset
|
529 samples and classifying them according to their relationship to reference transcripts. GffCompare has the following main functions: |
|
f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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diff
changeset
|
530 |
|
f99dd58de04f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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diff
changeset
|
531 - Merge structurally equivalent transcripts and transcript fragments (transfrags) across multiple samples |
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532 - Assess the accuracy of the assembled transcripts from an RNA-Seq sample by comparing it to known annotation |
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533 - Track, annotate, and report all structurally distinct transfrags across multiple samples |
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534 |
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535 The last two purposes require the user to provide a known reference annotation file that GffCompare then uses to classify all the transcripts in the input samples according to the |
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536 reference transcript that they most closely overlap. |
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537 |
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538 To assess the accuracy of transcriptome assemblies, GffCompare reports several accuracy metrics previously employed for gene prediction evaluation. These metrics include sensitivity |
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539 and precision as well as the number of novel or missed features, and the metrics are computed at various levels (base, exon, intron chain, transcript, or locus). |
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540 |
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541 ---- |
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542 |
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543 .. class:: infomark |
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544 |
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545 **Annotation mode** |
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546 |
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5
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547 When a single query GTF/GFF file is given as input for analysis, along with a reference annotation (-r option), GffCompare switches into annotation mode and it generates a *annotated |
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548 transcripts* file, allowing annotate transcripts by using a reference annotation. It should be noted that this file is not generated when options to remove "duplicated"/redundant transfrags are given (-D, -S, -C, -A, -X). |
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549 |
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550 ---- |
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551 |
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552 .. class:: infomark |
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553 |
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554 **Merging structually equivalent transcripts** |
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555 |
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556 When multiple input GTF/GFF files are provided, GffCompare reports a GTF file named *combined transcripts* that containing the union of all transfrags in each sample. If a transfrag with the same |
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557 exact intron chain is present in both samples, it is thus reported only once in the output file. |
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558 |
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559 **The "super-locus" concept** |
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560 |
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561 A super-locus is a region of the genome where predicted transcripts and reference transcripts get clustered together by exon overlaps. When multiple GFF files are provided as input to GffCompare, |
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562 this clustering is performed across all the input files. Due to the transitive nature of this clustering, these super-loci can occasionally get very large, sometimes merging a few distinct reference |
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563 gene regions together, especially if there is a lot of transcription or alignment noise around the individual gene regions. For each super-locus, GffCompare assigns a unique identifier with the XLOC prefix. |
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564 |
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565 ---- |
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566 |
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567 .. class:: infomark |
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568 |
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569 **Transcript accuracy estimation** |
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570 |
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571 GffCompare can be used to assess the accuracy of transcriptome assemblies produced by programs like StringTie 19 with respect to a known reference annotation. To this end, GffCompare |
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572 reports various statistics related to the accuracy of the input transcripts compared to the reference annotation in the *accuracy stats* file. |
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573 |
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574 Among these statistics are sensitivity and precision values computed at various levels (base, exon, intron chain, transcript, locus), which are calculated as: |
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575 |
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576 * Sensitivity = TP/(TP+FN) |
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577 * Precision = TP/(TP+FP) |
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578 |
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579 where TP stands for "true positives", or query features (bases, exons, introns, transcripts, etc.) that agree with the corresponding reference annotation features; FN means "false negatives", |
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580 i.e. features that are found in the reference annotation but are not present in the input data; FP (“false positives”) are features present in the input data but not confirmed by any reference |
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581 annotation data. Notice that FP+ TP amounts to the whole input set of query features in the input file. If multiple query GTF/GFF files are given as input, these metrics are computed separately |
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582 for each sample. |
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583 |
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584 Sensitivity and Precision values are estimated at various levels, which are largely an increasingly stringent way of evaluating the accuracy/correctness of a set of predicted transcripts (transfrags), |
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585 when compared to the reference annotation. The six different levels that GffCompare uses are described below: |
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586 |
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587 * **Base level**: At the base level, TP represents the number of exon bases that are reported at the same coordinate on both the query transcripts and any reference transcript, FN is the number of bases in reference data exons that are not covered at all by any of the query exons, and FP is the number of bases which are covered by predicted transcripts' exons but not covered by any reference transcript exons. |
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588 * **Exon level**: We define the TP, FN, and FP values at the exon level similar to the base level, but now the unit of comparison is the exon interval on the genome, i.e. if an exon of the predicted transcript overlaps and matches the boundaries of a reference transcript exon, then it is counted as a TP. |
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589 * **Intron Level**: Intron intervals are the units that are matched at the intron level, therefore each intron of the predicted transcript is checked against any introns of the reference transcripts in the same region and if there is one with the same exact start-end coordinates, it is counted as a TP. |
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590 * **Intron chain level**: At this level we count as a TP any query transcript for which all of its introns can be found, with the same exact intron coordinates as in a reference transcript that has the same number of introns. Matching all the introns at this level implies that all the internal exons also match, but this might not be true for the external boundaries of the terminal exons. |
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591 * **Transcript level**: Note that intron chain level values are calculated only by looking at multi-exon transcripts, so it completely ignores the single-exon transcripts, which can be quite numerous in a RNA-Seq experiment (possibly due to a lot of transcriptional and alignment noise). The transcript level considers single-exons as well. A TP at this level is defined as a full exon chain match between the predicted transcript and a reference transcript, where all internal exons match and the outer boundaries of the terminal query exons can only slightly differ from the reference exons (with at most 100 bases by default). Also GffCompare considers single-exon transcripts as matching an overlapping single-exon reference transcript if there is a significant overlap between the two (more than 80% of the longer transcript by default). |
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592 * **Locus level**: At this level GffCompare considers that an observed locus, defined as a cluster of exon-overlapping transcripts, matches a similarly built reference locus if at least one predicted transcript has a transcript level match with a reference transcript in the corresponding reference locus. |
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593 |
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594 ---- |
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595 |
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596 .. class:: infomark |
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597 |
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598 **Tracking transcripts** |
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599 |
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600 GffCompare can also be used to track all transcripts that are structurally equivalent among the different input files. GffCompare considers transcripts matching (or structurally equivalent) if all |
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601 their introns are identical. Note that matching transcripts are allowed to differ on the length of the first and last exons, since these lengths can usually vary across samples for the same biological transcript. |
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602 |
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603 A list of all matching transcripts is reported in a file called *tracking file* in which each row represents a transcript. The first column in this file represents a unique id assigned to that transcripts. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
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604 The second file represents the super-locus that contains that transcript. If a reference annotation is provided, the 3 rd and 4 th columns contain the reference annotation transcript that was found to be |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
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605 closest to the transcript and the classification code that specifies the relationship between these two transcripts, respectively. The rest of the columns show the corresponding |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
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606 transcript from each input file in order. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
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607 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
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608 **RefMap and TMAP files** |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
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609 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
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610 In order to quickly see which reference transcripts match which transcripts from a sample file, two other files, called *RefMap* and *TMAP* are also created for each query. The RefMap file is a tab-delimited file |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
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611 that has a row for each reference transcript that either fully or partially matches a transcript from the given input file. Conversely, the TMAP file has a row for each input transcript, while the columns in this |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
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612 file describe the most closely matching reference transcript for that transcript. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
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613 |
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614 ]]> |
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615 </help> |
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616 <expand macro="citations" /> |
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617 </tool> |