Mercurial > repos > iuc > gffcompare
annotate gffcompare.xml @ 5:46eaf3b078de draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
| author | iuc |
|---|---|
| date | Tue, 31 Aug 2021 08:29:34 +0000 |
| parents | 7eeb9fba4858 |
| children | 9e282a956012 |
| rev | line source |
|---|---|
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3
84845ad0d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
2
diff
changeset
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1 <tool id="gffcompare" name="GffCompare" version="@GFFCOMPARE_VERSION@"> |
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e52ca9ad69ca
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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46eaf3b078de
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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3 <xrefs> |
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46eaf3b078de
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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4 <xref type="bio.tools">gffcompare</xref> |
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46eaf3b078de
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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5 </xrefs> |
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84845ad0d35c
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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6 <macros> |
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84845ad0d35c
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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7 <token name="@GFFCOMPARE_VERSION@">0.11.2</token> |
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84845ad0d35c
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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8 </macros> |
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4
7eeb9fba4858
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit 95fe80d08fb14c4c344da4979290e72261e31ae5"
iuc
parents:
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diff
changeset
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9 <requirements> |
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84845ad0d35c
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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10 <requirement type="package" version="@GFFCOMPARE_VERSION@">gffcompare</requirement> |
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0
e52ca9ad69ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff
changeset
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11 </requirements> |
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e52ca9ad69ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff
changeset
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12 <version_command>gffcompare -v | awk '{print $2}'</version_command> |
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2
66f066ca5d60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit a5352fb7f073b0083b750c5cf7d283ebcc16b30d
iuc
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13 <command detect_errors="aggressive"><![CDATA[ |
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77c22296fb8e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
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14 #import re |
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84845ad0d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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15 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
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16 #set escaped_element_identifiers = [re.sub('[^\w\-]', '_', str(_.element_identifier)) for _ in $gffinputs] |
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77c22296fb8e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents:
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17 #for $input, $escaped_element_identifier in zip($gffinputs, $escaped_element_identifiers): |
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77c22296fb8e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents:
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18 ln -s '$input' '$escaped_element_identifier' && |
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77c22296fb8e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
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19 #end for |
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77c22296fb8e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents:
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changeset
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20 #if $seq_data.use_seq_data == "Yes": |
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77c22296fb8e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents:
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21 #if $seq_data.seq_source.index_source == "history": |
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77c22296fb8e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
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22 ln -s '$seq_data.seq_source.ref_file' ref_seq.fa && |
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77c22296fb8e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents:
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changeset
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23 #else: |
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77c22296fb8e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents:
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24 ln -s '${seq_data.seq_source.index.fields.path}' ref_seq.fa && |
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77c22296fb8e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents:
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changeset
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25 #end if |
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77c22296fb8e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
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26 #end if |
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0
e52ca9ad69ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
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27 |
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84845ad0d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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28 #if $annotation.use_ref_annotation == "Yes": |
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84845ad0d35c
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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29 #if $annotation.ref_source.ref_source_sel == "history": |
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84845ad0d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
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30 ln -s '$annotation.ref_source.reference_annotation' ref_annotation && |
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84845ad0d35c
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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31 #else |
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84845ad0d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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32 ln -s '$annotation.ref_source.index.fields.path' ref_annotation && |
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84845ad0d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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33 #end if |
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84845ad0d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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34 #end if |
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84845ad0d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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35 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
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36 gffcompare |
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77c22296fb8e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
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37 ## Use annotation reference? |
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77c22296fb8e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
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38 #if $annotation.use_ref_annotation == "Yes": |
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84845ad0d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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39 -r ref_annotation |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
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40 $annotation.ignore_nonoverlapping_reference |
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77c22296fb8e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
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41 $annotation.ignore_nonoverlapping_transfrags |
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84845ad0d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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42 $annotation.strict_match |
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84845ad0d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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43 #end if |
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84845ad0d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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44 #if $annotation.refmap_tmap == "": |
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84845ad0d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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45 -T |
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77c22296fb8e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
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46 #end if |
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e52ca9ad69ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
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47 |
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77c22296fb8e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
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48 ## Use sequence data? |
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77c22296fb8e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
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49 #if $seq_data.use_seq_data == "Yes": |
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77c22296fb8e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
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50 -s ref_seq.fa |
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77c22296fb8e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
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51 #end if |
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e52ca9ad69ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
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52 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
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53 $discard_single_exon |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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54 $discard_duplicates |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit 95fe80d08fb14c4c344da4979290e72261e31ae5"
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55 $no_merge |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit fc3616bd1463afef9681cd7c431ac29f79e37e74
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56 -e $max_dist_exon |
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77c22296fb8e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
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57 -d $max_dist_group |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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58 $chr_stats |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit a5352fb7f073b0083b750c5cf7d283ebcc16b30d
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59 -p '$adv_output.p' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit a5352fb7f073b0083b750c5cf7d283ebcc16b30d
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60 $adv_output.A |
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66f066ca5d60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit a5352fb7f073b0083b750c5cf7d283ebcc16b30d
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61 $adv_output.C |
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66f066ca5d60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit a5352fb7f073b0083b750c5cf7d283ebcc16b30d
iuc
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62 $adv_output.X |
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66f066ca5d60
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit a5352fb7f073b0083b750c5cf7d283ebcc16b30d
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63 $adv_output.K |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit fc3616bd1463afef9681cd7c431ac29f79e37e74
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64 |
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77c22296fb8e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit fc3616bd1463afef9681cd7c431ac29f79e37e74
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65 #for $escaped_element_identifier in $escaped_element_identifiers: |
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77c22296fb8e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
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66 '$escaped_element_identifier' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
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67 #end for |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit a5352fb7f073b0083b750c5cf7d283ebcc16b30d
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68 |
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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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e52ca9ad69ca
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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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit fc3616bd1463afef9681cd7c431ac29f79e37e74
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71 <param format="gtf" name="gffinputs" type="data" label="GTF inputs for comparison" help="" multiple="true" /> |
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e52ca9ad69ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
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72 <conditional name="annotation"> |
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e52ca9ad69ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
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73 <param label="Use Reference Annotation" name="use_ref_annotation" type="select"> |
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e52ca9ad69ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
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74 <option value="No">No</option> |
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e52ca9ad69ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
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75 <option value="Yes">Yes</option> |
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e52ca9ad69ca
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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e52ca9ad69ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
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77 <when value="Yes"> |
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84845ad0d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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78 <conditional name="ref_source"> |
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79 <param label="Choose the source for the reference annotation" name="ref_source_sel" type="select"> |
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80 <option value="cached">Locally cached</option> |
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81 <option value="history">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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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" format="gff3,gtf" help="Requires an annotation file in GFF3 or GTF format." label="Reference Annotation" name="reference_annotation" type="data" /> |
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93 </when> |
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94 </conditional> |
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95 <param argument="-R" falsevalue="" help="consider only the reference transcripts that overlap any of the input transfrags (Sn correction)" label="Ignore reference transcripts that are not overlapped by any input transfrags" name="ignore_nonoverlapping_reference" truevalue="-R" type="boolean" /> |
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96 <param argument="-Q" falsevalue="" help="consider only the input transcripts that overlap any of the reference transcripts (Sp correction). Warning: this will discard all 'novel' loci!" label="Ignore input transcripts that are not overlapped by any reference transcripts" name="ignore_nonoverlapping_transfrags" truevalue="-Q" type="boolean" /> |
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97 <param argument="--strict-match" name="strict_match" type="boolean" checked="false" truevalue="--strict-match" falsevalue="" label="the match code '=' is only assigned when all exon boundaries match" help="code '~' is assigned for intron chain match or single-exon" /> |
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98 <param argument="-T" name="refmap_tmap" label="Generate tmap or refmap file for each input file" type="select" multiple="True"> |
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99 <option value="refmap" selected="True">refmap</option> |
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100 <option value="tmap" selected="True">tmap</option> |
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101 </param> |
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102 </when> |
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103 <when value="No"> |
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104 <param argument="-T" name="refmap_tmap" label="Generate tmap file for each input file" type="select" multiple="True"> |
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105 <option value="tmap" selected="True">tmap</option> |
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106 </param> |
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0
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107 </when> |
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108 </conditional> |
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109 <conditional name="seq_data"> |
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110 <param help="Use sequence data for some optional classification functions, including the addition of the p_id attribute required by Cuffdiff." label="Use Sequence Data" name="use_seq_data" type="select"> |
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111 <option value="No">No</option> |
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112 <option value="Yes">Yes</option> |
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113 </param> |
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114 <when value="No"/> |
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115 <when value="Yes"> |
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116 <conditional name="seq_source"> |
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117 <param label="Choose the source for the reference sequence" name="index_source" type="select"> |
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118 <option value="cached">Locally cached</option> |
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119 <option value="history">History</option> |
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120 </param> |
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121 <when value="cached"> |
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122 <param argument="-s" label="Using reference genome" name="index" type="select"> |
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123 <options from_data_table="fasta_indexes"> |
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124 <filter column="dbkey" key="dbkey" ref="gffinputs" type="data_meta" /> |
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125 </options> |
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126 <validator message="No reference genome is available for the build associated with the selected input dataset" type="no_options" /> |
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127 </param> |
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128 </when> |
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129 <when value="history"> |
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130 <param argument="-s" format="fasta" label="Using reference file" name="ref_file" type="data" /> |
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131 </when> |
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132 </conditional> |
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133 </when> |
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134 </conditional> |
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135 <param name="discard_single_exon" argument="-M/-N" type="select" label="Discard single-exon transcripts" help="If -S and also --strict-match is given, exact matching of all exon boundaries is required"> |
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136 <option selected="True" value="">No</option> |
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137 <option value="-M">Discard single-exon transfrags and reference transcripts</option> |
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138 <option value="-N">Discard single-exon reference transcripts</option> |
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139 </param> |
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140 <param label="Discard duplicates" name="discard_duplicates" type="select"> |
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141 <option value="">None</option> |
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142 <option value="-D">discard 'duplicate' query transfrags within a single sample (-D)</option> |
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143 <option value="-S">Only discard 'duplicate' query or reference transcripts if their boundaries are fully contained within other, larger or identical transfrags (-S)</option> |
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144 </param> |
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145 <param name="no_merge" argument="--no-merge" type="boolean" checked="false" truevalue="--no-merge" falsevalue="" label="Disable close-exon merging" help="Default: merge exons separated by 'introns' shorter than 5 bases" /> |
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146 <param argument="-e" help="max. distance (range) allowed from free ends of terminal exons of reference transcripts when assessing exon accuracy. Default: 100" label="Max. Distance for assessing exon accuracy" name="max_dist_exon" type="integer" value="100" /> |
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147 <param argument="-d" help="max. distance (range) for grouping transcript start sites. Default: 100" label="Max distance for transcript grouping" name="max_dist_group" type="integer" value="100" /> |
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148 <param name="chr_stats" argument="--chr-stats" type="boolean" checked="false" truevalue="--chr-stats" falsevalue="" label="Show summary and accuracy data separately for each reference sequence in the transcript accuracy data set" /> |
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149 <section name="adv_output" title="Options for the combined GTF output file"> |
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150 <param argument="-p" type="text" value="TCONS" label="name prefix for consensus transcripts" help="for combined.gtf" /> |
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151 <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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152 <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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153 <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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154 <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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155 </section> |
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156 </inputs> |
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157 <outputs> |
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158 <data format="txt" from_work_dir="gffcmp.stats" label="${tool.name} on ${on_string}: transcript accuracy" name="transcripts_stats" /> |
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159 <data format="tabular" from_work_dir="gffcmp.loci" label="${tool.name} on ${on_string}: loci" name="transcripts_loci" /> |
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160 <data format="tabular" from_work_dir="gffcmp.tracking" label="${tool.name} on ${on_string}: data ${gffinputs[0].hid} tracking file" name="transcripts_tracking" /> |
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161 <data format="gtf" from_work_dir="gffcmp.combined.gtf" label="${tool.name} on ${on_string}: combined transcripts" name="transcripts_combined"> |
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162 <filter>(isinstance(gffinputs, list) and len(gffinputs) > 1) or annotation['use_ref_annotation'] == "No"</filter> |
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163 </data> |
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164 <data format="gtf" from_work_dir="gffcmp.annotated.gtf" label="${tool.name} on ${on_string}: annotated transcripts" name="transcripts_annotated"> |
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165 <filter>not (isinstance(gffinputs, list) and len(gffinputs) > 1) and annotation['use_ref_annotation'] == "Yes"</filter> |
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166 </data> |
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167 <collection name="refmap_output" type="list" label="${tool.name} on ${on_string}: refmap"> |
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168 <discover_datasets pattern="gffcmp\.(?P<designation>.+)\.refmap" ext="tabular" /> |
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169 <filter>annotation['refmap_tmap'] != None and 'refmap' in annotation['refmap_tmap']</filter> |
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170 </collection> |
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171 <collection name="tmap_output" type="list" label="${tool.name} on ${on_string}: tmap"> |
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172 <discover_datasets pattern="gffcmp\.(?P<designation>.+)\.tmap" ext="tabular" /> |
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173 <filter>annotation['refmap_tmap'] != None and 'tmap' in annotation['refmap_tmap']</filter> |
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174 </collection> |
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175 </outputs> |
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176 <tests> |
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177 <!-- 2 inputs, no reference, default options --> |
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178 <test expect_num_outputs="5"> |
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179 <param ftype="gtf" name="gffinputs" value="gffcompare_in1.gtf,gffcompare_in2.gtf" /> |
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180 <conditional name="annotation"> |
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181 <param name="use_ref_annotation" value="No" /> |
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182 </conditional> |
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183 <conditional name="seq_data"> |
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184 <param name="use_seq_data" value="No" /> |
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185 </conditional> |
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186 <assert_command> |
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187 <not_has_text text="-R " /> |
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188 <not_has_text text="-Q " /> |
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189 <not_has_text text="--strict-match " /> |
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190 <not_has_text text="-T " /> |
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191 <has_text_matching expression="^.*gffcompare((?!-s).)*$" /> <!-- since ln also has -s a more complicated regexp is needed here to check if -s is not set --> |
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192 <not_has_text text="-M " /> |
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193 <not_has_text text="-N " /> |
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194 <has_text text="-e 100 " /> |
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195 <has_text text="-d 100 " /> |
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196 <not_has_text text="-D " /> |
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197 <not_has_text text="--no-merge " /> |
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198 <has_text text="-p 'TCONS' " /> |
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199 <not_has_text text="-C " /> |
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200 <not_has_text text="-A " /> |
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201 <not_has_text text="-X " /> |
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202 <not_has_text text="-K " /> |
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203 </assert_command> |
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204 <output file="gffcompare_out1.stats" name="transcripts_stats" /> |
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205 <output file="gffcompare_out1.loci" name="transcripts_loci" /> |
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206 <output file="gffcompare_out1.tracking" name="transcripts_tracking" /> |
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207 <output file="gffcompare_out1.gtf" name="transcripts_combined" /> |
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208 <output_collection name="tmap_output" type="list" count="2"/> |
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209 </test> |
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210 <!-- 2 inputs, no reference, with refsequence, default options (but disable tmap output) --> |
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211 <test expect_num_outputs="4"> |
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212 <param ftype="gtf" name="gffinputs" value="gffcompare_in1.gtf,gffcompare_in2.gtf" /> |
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213 <conditional name="annotation"> |
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214 <param name="use_ref_annotation" value="No" /> |
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215 <param name="refmap_tmap" value=""/> |
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216 </conditional> |
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217 <conditional name="seq_data"> |
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218 <param name="use_seq_data" value="Yes" /> |
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219 <conditional name="seq_source"> |
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220 <param name="index_source" value="history"/> |
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221 <param name="ref_file" ftype="fasta" value="sequence.fa"/> |
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222 </conditional> |
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223 </conditional> |
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224 <assert_command> |
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225 <not_has_text text="-R " /> |
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226 <not_has_text text="-Q " /> |
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227 <has_text text="-T " /> |
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228 <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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229 <not_has_text text="-M " /> |
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230 <not_has_text text="-N " /> |
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231 <has_text text="-e 100 " /> |
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232 <has_text text="-d 100 " /> |
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233 <has_text text="-p 'TCONS' " /> |
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234 <not_has_text text="-C " /> |
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235 <not_has_text text="-A " /> |
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236 <not_has_text text="-X " /> |
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237 <not_has_text text="-K " /> |
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238 </assert_command> |
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239 <output file="gffcompare_out1.stats" name="transcripts_stats" compare="sim_size" /> |
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240 <output file="gffcompare_out1.loci" name="transcripts_loci" compare="sim_size" /> |
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241 <output file="gffcompare_out1.tracking" name="transcripts_tracking" compare="sim_size" /> |
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242 <output file="gffcompare_out1.gtf" name="transcripts_combined" compare="sim_size" /> |
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243 </test> |
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244 <!-- 2 inputs, no reference, with cached refsequence, default options (but disable tmap output) --> |
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245 <test expect_num_outputs="4"> |
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246 <param ftype="gtf" name="gffinputs" value="gffcompare_in1.gtf,gffcompare_in2.gtf" dbkey="hg17" /> |
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247 <conditional name="annotation"> |
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248 <param name="use_ref_annotation" value="No" /> |
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249 <param name="refmap_tmap" value=""/> |
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250 </conditional> |
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251 <conditional name="seq_data"> |
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252 <param name="use_seq_data" value="Yes" /> |
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253 <conditional name="seq_source"> |
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254 <param name="index_source" value="cached"/> |
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255 <param name="index" value="test_buildid"/> |
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256 </conditional> |
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257 </conditional> |
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258 <assert_command> |
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259 <not_has_text text="-R " /> |
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260 <not_has_text text="-Q " /> |
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261 <has_text text="-T " /> |
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262 <has_text_matching expression="gffcompare.*-s " /> |
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263 <not_has_text text="-M " /> |
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264 <not_has_text text="-N " /> |
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265 <has_text text="-e 100 " /> |
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266 <has_text text="-d 100 " /> |
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267 <has_text text="-p 'TCONS' " /> |
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268 <not_has_text text="-C " /> |
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269 <not_has_text text="-A " /> |
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270 <not_has_text text="-X " /> |
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271 <not_has_text text="-K " /> |
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272 </assert_command> |
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273 <output file="gffcompare_out1.stats" name="transcripts_stats" compare="sim_size" /> |
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274 <output file="gffcompare_out1.loci" name="transcripts_loci" compare="sim_size" /> |
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275 <output file="gffcompare_out1.tracking" name="transcripts_tracking" compare="sim_size" /> |
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276 <output file="gffcompare_out1.gtf" name="transcripts_combined" compare="sim_size" /> |
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277 </test> |
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278 <!-- 2 inputs and reference, default options --> |
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279 <test expect_num_outputs="6"> |
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280 <param ftype="gtf" name="gffinputs" value="gffcompare_in1.gtf,gffcompare_in2.gtf" /> |
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281 <conditional name="annotation"> |
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282 <param name="use_ref_annotation" value="Yes" /> |
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283 <conditional name="ref_source"> |
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284 <param name="ref_source_sel" value="history"/> |
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285 <param ftype="gtf" name="reference_annotation" value="gffcompare_in3.gtf" /> |
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286 </conditional> |
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287 </conditional> |
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288 <conditional name="seq_data"> |
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289 <param name="use_seq_data" value="No" /> |
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290 </conditional> |
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291 <assert_command> |
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292 <not_has_text text="-R " /> |
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293 <not_has_text text="-Q " /> |
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294 <not_has_text text="--strict-match " /> |
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295 <not_has_text text="-T " /> |
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296 <not_has_text text="-M " /> |
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297 <not_has_text text="-N " /> |
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298 <has_text text="-e 100 " /> |
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299 <has_text text="-d 100 " /> |
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300 <not_has_text text="-D " /> |
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301 <not_has_text text="--no-merge " /> |
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302 <not_has_text text="--chr-stats" /> |
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303 <has_text text="-p 'TCONS' " /> |
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304 <not_has_text text="-C " /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
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305 <not_has_text text="-A " /> |
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306 <not_has_text text="-X " /> |
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307 <not_has_text text="-K " /> |
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308 </assert_command> |
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4
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309 <output file="gffcompare_out2.stats" name="transcripts_stats" /> |
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310 <output file="gffcompare_out2.loci" name="transcripts_loci" compare="sim_size" /> |
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311 <output file="gffcompare_out2.tracking" name="transcripts_tracking" /> |
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312 <output file="gffcompare_out2.gtf" name="transcripts_combined" /> |
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313 <output_collection name="refmap_output" type="list" count="2"> |
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314 <element name="gffcompare_in1_gtf" file="gffcompare_out2-1.refmap" ftype="tabular" /> |
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315 <element name="gffcompare_in2_gtf" file="gffcompare_out2-2.refmap" ftype="tabular" /> |
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316 </output_collection> |
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317 <output_collection name="tmap_output" type="list" count="2"> |
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318 <element name="gffcompare_in1_gtf" file="gffcompare_out2-1.tmap" ftype="tabular" /> |
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319 <element name="gffcompare_in2_gtf" file="gffcompare_out2-2.tmap" ftype="tabular" /> |
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1
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320 </output_collection> |
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0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
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321 </test> |
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322 <!-- 2 inputs and reference (cached), non default options, only refmap output --> |
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323 <test expect_num_outputs="5"> |
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324 <param ftype="gtf" name="gffinputs" value="gffcompare_in1.gtf,gffcompare_in2.gtf" dbkey="hg17" /> |
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325 <conditional name="annotation"> |
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326 <param name="use_ref_annotation" value="Yes" /> |
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327 <conditional name="ref_source"> |
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328 <param name="ref_source_sel" value="cached"/> |
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329 <param name="index" value="test_buildid"/> |
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330 </conditional> |
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331 <param name="ignore_nonoverlapping_reference" value="Yes" /> |
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332 <param name="ignore_nonoverlapping_transfrags" value="Yes" /> |
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333 <param name="strict_match" value="--strict-match" /> |
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334 <param name="refmap_tmap" value="refmap" /> |
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335 </conditional> |
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336 <conditional name="seq_data"> |
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337 <param name="use_seq_data" value="No" /> |
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338 </conditional> |
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339 <param name="discard_single_exon" value="-M"/> |
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340 <param name="discard_duplicates" value="-D"/> |
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341 <param name="no_merge" value="--no-merge" /> |
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342 <param name="max_dist_exon" value="101" /> |
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343 <param name="max_dist_group" value="99" /> |
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344 <param name="chr_stats" value="--chr-stats" /> |
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345 <assert_command> |
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346 <has_text text="-R " /> |
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347 <has_text text="-Q " /> |
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348 <has_text text="--strict-match " /> |
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349 <not_has_text text="-T " /> |
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350 <has_text text="-M " /> |
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351 <not_has_text text="-N " /> |
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352 <has_text text="-e 101 " /> |
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353 <has_text text="-d 99 " /> |
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354 <has_text text="-D " /> |
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355 <has_text text="--no-merge " /> |
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356 <has_text text="--chr-stats" /> |
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357 <has_text text="-p 'TCONS' " /> |
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358 <not_has_text text="-C " /> |
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359 <not_has_text text="-A " /> |
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360 <not_has_text text="-X " /> |
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361 <not_has_text text="-K " /> |
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362 </assert_command> |
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363 <output file="gffcompare_out2.stats" name="transcripts_stats" compare="sim_size" /> |
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364 <output file="gffcompare_out2.loci" name="transcripts_loci" compare="sim_size" /> |
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365 <output file="gffcompare_out2.tracking" name="transcripts_tracking" compare="sim_size" /> |
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366 <output file="gffcompare_out2.gtf" name="transcripts_combined" compare="sim_size" delta="50000"/> |
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367 <output_collection name="refmap_output" type="list" count="0"/> <!-- because of -M no refmaps are created --> |
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368 </test> |
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369 <!-- 2 inputs and reference, non default advanced options, only tmap output --> |
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370 <test expect_num_outputs="5"> |
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371 <param ftype="gtf" name="gffinputs" value="gffcompare_in1.gtf,gffcompare_in2.gtf" /> |
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372 <conditional name="annotation"> |
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373 <param name="use_ref_annotation" value="Yes" /> |
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374 <conditional name="ref_source"> |
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375 <param name="ref_source_sel" value="history"/> |
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376 <param ftype="gtf" name="reference_annotation" value="gffcompare_in3.gtf" /> |
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377 </conditional> |
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378 <param name="refmap_tmap" value="tmap" /> |
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379 </conditional> |
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380 <conditional name="seq_data"> |
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381 <param name="use_seq_data" value="No" /> |
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84845ad0d35c
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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382 </conditional> |
|
84845ad0d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
383 <section name="adv_output"> |
|
84845ad0d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
384 <param name="p" value="OTHER" /> |
|
84845ad0d35c
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 <param name="C" value="-C" /> |
|
84845ad0d35c
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="A" value="-A" /> |
|
84845ad0d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
387 <param name="X" value="-X" /> |
|
84845ad0d35c
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 <param name="K" value="-K" /> |
|
84845ad0d35c
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 </section> |
|
84845ad0d35c
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 <assert_command> |
|
84845ad0d35c
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 <not_has_text text="-R " /> |
|
84845ad0d35c
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="-Q " /> |
|
4
7eeb9fba4858
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit 95fe80d08fb14c4c344da4979290e72261e31ae5"
iuc
parents:
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diff
changeset
|
393 <not_has_text text="--strict-match " /> |
|
3
84845ad0d35c
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="-T " /> |
|
84845ad0d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
395 <not_has_text text="-M " /> |
|
84845ad0d35c
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 <not_has_text text="-N " /> |
|
84845ad0d35c
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="-e 100 " /> |
|
84845ad0d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
2
diff
changeset
|
398 <has_text text="-d 100 " /> |
|
4
7eeb9fba4858
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit 95fe80d08fb14c4c344da4979290e72261e31ae5"
iuc
parents:
3
diff
changeset
|
399 <not_has_text text="-D " /> |
|
7eeb9fba4858
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit 95fe80d08fb14c4c344da4979290e72261e31ae5"
iuc
parents:
3
diff
changeset
|
400 <not_has_text text="--no-merge " /> |
|
7eeb9fba4858
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit 95fe80d08fb14c4c344da4979290e72261e31ae5"
iuc
parents:
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diff
changeset
|
401 <not_has_text text="--chr-stats" /> |
|
7eeb9fba4858
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit 95fe80d08fb14c4c344da4979290e72261e31ae5"
iuc
parents:
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diff
changeset
|
402 <has_text text="-p 'OTHER' " /> |
|
3
84845ad0d35c
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 <has_text text="-C " /> |
|
84845ad0d35c
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 <has_text text="-A " /> |
|
84845ad0d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
405 <has_text text="-X " /> |
|
84845ad0d35c
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 <has_text text="-K " /> |
|
84845ad0d35c
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 </assert_command> |
|
84845ad0d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
408 <output file="gffcompare_out2.stats" name="transcripts_stats" compare="sim_size" /> |
|
84845ad0d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
409 <output file="gffcompare_out2.loci" name="transcripts_loci" compare="sim_size" /> |
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84845ad0d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
410 <output file="gffcompare_out2.tracking" name="transcripts_tracking" compare="sim_size" /> |
|
84845ad0d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
411 <output file="gffcompare_out2.gtf" name="transcripts_combined" compare="sim_size" delta="50000"/> |
|
84845ad0d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
412 <output_collection name="tmap_output" type="list" count="2"/> |
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84845ad0d35c
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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413 </test> |
|
84845ad0d35c
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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414 <!-- 2 inputs and reference, default options, no tmap or refmap output --> |
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84845ad0d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
415 <test expect_num_outputs="4"> |
|
84845ad0d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
416 <param ftype="gtf" name="gffinputs" value="gffcompare_in1.gtf,gffcompare_in2.gtf" /> |
|
84845ad0d35c
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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417 <conditional name="annotation"> |
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84845ad0d35c
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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418 <param name="use_ref_annotation" value="Yes" /> |
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84845ad0d35c
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 <conditional name="ref_source"> |
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84845ad0d35c
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 name="ref_source_sel" value="history"/> |
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84845ad0d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
421 <param ftype="gtf" name="reference_annotation" value="gffcompare_in3.gtf" /> |
|
84845ad0d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
422 </conditional> |
|
84845ad0d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
423 <param name="refmap_tmap" value="" /> |
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84845ad0d35c
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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424 </conditional> |
|
84845ad0d35c
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 name="seq_data"> |
|
84845ad0d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
426 <param name="use_seq_data" value="No" /> |
|
84845ad0d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
427 </conditional> |
|
84845ad0d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
428 <assert_command> |
|
84845ad0d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
429 <not_has_text text="-R " /> |
|
84845ad0d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
430 <not_has_text text="-Q " /> |
|
4
7eeb9fba4858
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit 95fe80d08fb14c4c344da4979290e72261e31ae5"
iuc
parents:
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diff
changeset
|
431 <not_has_text text="--strict-match " /> |
|
3
84845ad0d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
432 <has_text text="-T " /> |
|
84845ad0d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
433 <not_has_text text="-M " /> |
|
84845ad0d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
434 <not_has_text text="-N " /> |
|
84845ad0d35c
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 <has_text text="-e 100 " /> |
|
84845ad0d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
2
diff
changeset
|
436 <has_text text="-d 100 " /> |
|
4
7eeb9fba4858
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit 95fe80d08fb14c4c344da4979290e72261e31ae5"
iuc
parents:
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diff
changeset
|
437 <not_has_text text="-D " /> |
|
7eeb9fba4858
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit 95fe80d08fb14c4c344da4979290e72261e31ae5"
iuc
parents:
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diff
changeset
|
438 <not_has_text text="--no-merge " /> |
|
7eeb9fba4858
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit 95fe80d08fb14c4c344da4979290e72261e31ae5"
iuc
parents:
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diff
changeset
|
439 <not_has_text text="--chr-stats" /> |
|
7eeb9fba4858
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit 95fe80d08fb14c4c344da4979290e72261e31ae5"
iuc
parents:
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diff
changeset
|
440 <has_text text="-p 'TCONS' " /> |
|
3
84845ad0d35c
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 <not_has_text text="-C " /> |
|
84845ad0d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
442 <not_has_text text="-A " /> |
|
84845ad0d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
443 <not_has_text text="-X " /> |
|
84845ad0d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
2
diff
changeset
|
444 <not_has_text text="-K " /> |
|
84845ad0d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
445 </assert_command> |
|
4
7eeb9fba4858
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit 95fe80d08fb14c4c344da4979290e72261e31ae5"
iuc
parents:
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diff
changeset
|
446 <output file="gffcompare_out2.stats" name="transcripts_stats" lines_diff="2" /> |
|
7eeb9fba4858
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit 95fe80d08fb14c4c344da4979290e72261e31ae5"
iuc
parents:
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diff
changeset
|
447 <output file="gffcompare_out2.loci" name="transcripts_loci" compare="sim_size" /> |
|
3
84845ad0d35c
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 <output file="gffcompare_out2.tracking" name="transcripts_tracking" /> |
|
84845ad0d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
2
diff
changeset
|
449 <output file="gffcompare_out2.gtf" name="transcripts_combined" /> |
|
84845ad0d35c
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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450 </test> |
|
84845ad0d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
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diff
changeset
|
451 |
|
1
77c22296fb8e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents:
0
diff
changeset
|
452 <test expect_num_outputs="4"> |
|
77c22296fb8e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents:
0
diff
changeset
|
453 <param ftype="gtf" name="gffinputs" value="gffcompare_in4.gtf" /> |
|
77c22296fb8e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents:
0
diff
changeset
|
454 <conditional name="annotation"> |
|
3
84845ad0d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
2
diff
changeset
|
455 <param name="use_ref_annotation" value="Yes" /> |
|
84845ad0d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
2
diff
changeset
|
456 <conditional name="ref_source"> |
|
84845ad0d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
2
diff
changeset
|
457 <param name="ref_source_sel" value="history"/> |
|
84845ad0d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
2
diff
changeset
|
458 <param ftype="gtf" name="reference_annotation" value="gffcompare_in5.gtf" /> |
|
84845ad0d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
2
diff
changeset
|
459 </conditional> |
|
1
77c22296fb8e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents:
0
diff
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460 <param name="ignore_nonoverlapping_reference" value="Yes" /> |
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461 <param name="ignore_nonoverlapping_transfrags" value="No" /> |
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462 <param name="refmap_tmap" value="" /> |
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463 </conditional> |
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464 <param name="use_seq_data" value="No" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
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465 <param name="discard_single_exon" value="" /> |
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466 <param name="max_dist_exon" value="100" /> |
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467 <param name="max_dist_group" value="100" /> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit 95fe80d08fb14c4c344da4979290e72261e31ae5"
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468 <output file="gffcompare_out3.stats" name="transcripts_stats"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit 95fe80d08fb14c4c344da4979290e72261e31ae5"
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469 <output file="gffcompare_out3.loci" name="transcripts_loci" compare="sim_size" /> |
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470 <output file="gffcompare_out3.tracking" name="transcripts_tracking" /> |
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471 <output file="gffcompare_out3.gtf" name="transcripts_annotated" /> |
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472 </test> |
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473 </tests> |
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474 <help> |
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475 <![CDATA[ |
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476 **GffCompare Overview** |
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477 |
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478 ## GffCompare |
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479 * compare and evaluate the accuracy of RNA-Seq transcript assemblers (Cufflinks, Stringtie). |
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480 * collapse (merge) duplicate transcripts from multiple GTF/GFF3 files (e.g. resulted from assembly of different samples) |
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481 * classify transcripts from one or multiple GTF/GFF3 files as they relate to reference transcripts provided in a |
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482 annotation file (also in GTF/GFF3 format) |
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483 |
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484 More information can be found here: https://ccb.jhu.edu/software/stringtie/gffcompare.shtml |
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485 |
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486 The original form of this program is also distributed as part of the Cufflinks suite, under the name "CuffCompare" |
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487 (see manual: http://cole-trapnell-lab.github.io/cufflinks/cuffcompare/). Most of the options and parameters of CuffCompare |
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488 are supported by GffCompare, while new features will likely be added to GffCompare in the future. |
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489 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit a5352fb7f073b0083b750c5cf7d283ebcc16b30d
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490 A notable difference of GffCompare is that when a single query GTF/GFF file is given as input, along with a reference annotation (-r option), |
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491 gffcompare switches into "annotation mode" and it generates a .annotated.gtf file instead of the .merged.gtf produced by CuffCompare with the |
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492 same parameters. This file has the same general format as CuffCompare's .merged.gtf file (with "class codes" assigned to transcripts as per |
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493 their relationship with the matching/overlapping reference transcript), but the original transcript IDs are preserved, so gffcompare can thus |
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494 be used as a simple way of annotating a set of transcripts. |
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495 |
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496 Another important difference is that the input transcripts are no longer discarded when they are found to be "intron redundant", i.e. |
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497 contained within other, longer isoforms. CuffCompare had the -G option to prevent collapsing of such intron redundant isoforms into |
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498 their longer "containers", but GffCompare has made this the default mode of operation (hence the -G option is no longer needed |
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499 and is simply ignored when given). |
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500 ]]> |
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501 </help> |
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502 <citations> |
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503 <citation type="doi">10.1038/nbt.1621</citation> |
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504 </citations> |
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505 </tool> |