Mercurial > repos > iuc > gffcompare
annotate gffcompare.xml @ 8:3b8c94e2674a draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
| author | iuc |
|---|---|
| date | Tue, 13 May 2025 19:03:30 +0000 |
| parents | 832c22dd7578 |
| children |
| rev | line source |
|---|---|
|
8
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
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changeset
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1 <tool id="gffcompare" name="GffCompare" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.2"> |
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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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9e282a956012
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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3 <macros> |
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9e282a956012
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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4 <import>macros.xml</import> |
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9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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5 </macros> |
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5
46eaf3b078de
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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6 <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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changeset
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7 <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
parents:
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changeset
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8 </xrefs> |
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8
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
7
diff
changeset
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9 <expand macro="requirements"/> |
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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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10 <version_command>gffcompare -v | awk '{print $2}'</version_command> |
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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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11 <command detect_errors="aggressive"><![CDATA[ |
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9e282a956012
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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12 #import re |
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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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13 |
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6
9e282a956012
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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14 #set escaped_element_identifiers = [re.sub('[^\w\-]', '_', str(_.element_identifier)) for _ in $gffinputs] |
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9e282a956012
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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15 #for $input, $escaped_element_identifier in zip($gffinputs, $escaped_element_identifiers): |
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9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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diff
changeset
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16 ln -s '$input' '$escaped_element_identifier' && |
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9e282a956012
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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9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
5
diff
changeset
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18 #if $conditional_annotation.selector == "yes": |
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9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
5
diff
changeset
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19 #if $conditional_annotation.ref_source.selector == "history": |
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9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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diff
changeset
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20 ln -s '$conditional_annotation.ref_source.reference_annotation' reference_annotation && |
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9e282a956012
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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21 #else: |
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9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
5
diff
changeset
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22 ln -s '${conditional_annotation.ref_source.index.fields.path}' reference_annotation && |
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9e282a956012
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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23 #end if |
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9e282a956012
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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9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
5
diff
changeset
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25 #if $seq_data.selector == "Yes": |
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9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
5
diff
changeset
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26 #if $seq_data.seq_source.index_source == "history": |
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9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
5
diff
changeset
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27 ln -s '$seq_data.seq_source.ref_genome' ref_seq.fa && |
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9e282a956012
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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28 samtools faidx ref_seq.fa && |
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9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
5
diff
changeset
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29 #else: |
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9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
5
diff
changeset
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30 ln -s '${seq_data.seq_source.index.fields.path}' ref_seq.fa && |
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9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
5
diff
changeset
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31 #end if |
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9e282a956012
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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32 #end if |
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9e282a956012
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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9e282a956012
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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34 #if $conditional_annotation.selector == "yes": |
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9e282a956012
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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9e282a956012
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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36 $conditional_annotation.R |
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9e282a956012
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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9e282a956012
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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9e282a956012
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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9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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40 -e $conditional_annotation.conditional_strict.e |
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9e282a956012
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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9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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42 $conditional_annotation.discard_single_exon |
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9e282a956012
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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9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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44 #if $conditional_annotation.conditional_duplication.selector == "-D" |
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9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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45 $conditional_annotation.conditional_duplication.S |
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9e282a956012
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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9e282a956012
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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9e282a956012
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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9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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49 $refmap_tmap |
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9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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50 #if $seq_data.selector == "Yes": |
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9e282a956012
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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9e282a956012
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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9e282a956012
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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9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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54 $chr_stats |
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9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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55 -p '$adv_output.p' |
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9e282a956012
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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9e282a956012
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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9e282a956012
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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9e282a956012
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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9e282a956012
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 $escaped_element_identifiers: |
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9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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61 '$escaped_element_identifier' |
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9e282a956012
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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9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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63 #if len($gffinputs) == 1 and $refmap_tmap == 'true' |
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9e282a956012
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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9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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65 #if $seq_data.selector == "Yes" |
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9e282a956012
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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9e282a956012
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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9e282a956012
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
77c22296fb8e
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 c62791a7ff6fef8cb19b84465662d13effaffe1d
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71 <param format="gtf,gff3" name="gffinputs" type="data" label="GTF inputs for comparison" multiple="true"/> |
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9e282a956012
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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9e282a956012
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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9e282a956012
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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9e282a956012
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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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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9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
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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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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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142 </param> |
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143 <when value="no"/> |
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144 <when value="yes"> |
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145 <conditional name="seq_source"> |
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3
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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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6
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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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8
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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 ${on_string}: RefMap Collection"> |
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194 <discover_datasets pattern="gffcmp\.(?P<designation>.+)\.refmap" ext="tabular"/> |
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195 <filter>conditional_annotation['selector'] == 'yes'</filter> |
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196 <filter>len(gffinputs) > 1</filter> |
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197 <filter>refmap_tmap</filter> |
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198 </collection> |
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199 <data name="refmap_output" format="tabular" from_work_dir="output.refmap" label="${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 ${on_string}: TMAP Collection"> |
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205 <discover_datasets pattern="gffcmp\.(?P<designation>.+)\.tmap" ext="tabular"/> |
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206 <filter>refmap_tmap</filter> |
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207 <filter>len(gffinputs) > 1</filter> |
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208 </collection> |
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209 <data name="tmap_output" format="tabular" from_work_dir="output.tmap" label="${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 ${on_string}: tracking file"/> |
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216 </outputs> |
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217 <tests> |
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218 <!-- Test 01: 2 inputs, no reference, default options --> |
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219 <test expect_num_outputs="5"> |
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220 <param ftype="gtf" name="gffinputs" value="gffcompare_in1.gtf,gffcompare_in2.gtf"/> |
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221 <conditional name="conditional_annotation"> |
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222 <param name="selector" value="no"/> |
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223 </conditional> |
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224 <conditional name="seq_data"> |
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225 <param name="selector" value="no"/> |
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226 </conditional> |
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227 <assert_command> |
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228 <not_has_text text="-R "/> |
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229 <not_has_text text="-Q "/> |
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230 <not_has_text text="--strict-match "/> |
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231 <not_has_text text="-T "/> |
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232 <has_text_matching expression="^.*gffcompare((?!-s).)*$"/> <!-- since ln also has -s a more complicated regexp is needed here to check if -s is not set --> |
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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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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
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242 <not_has_text text="-K "/> |
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243 </assert_command> |
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244 <output name="transcripts_stats" ftype="txt"> |
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245 <assert_contents> |
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246 <has_line line="#gffcompare -V -d 100 -p TCONS gffcompare_in1_gtf gffcompare_in2_gtf"/> |
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247 <has_line line=" Total union super-loci across all input datasets: 7 "/> |
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248 <has_n_lines n="15"/> |
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249 </assert_contents> |
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250 </output> |
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251 <output name="transcripts_loci" ftype="tabular"> |
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252 <assert_contents> |
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253 <has_n_lines n="7"/> |
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254 </assert_contents> |
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255 </output> |
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256 <output name="transcripts_tracking"> |
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257 <assert_contents> |
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258 <has_n_lines n="9"/> |
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259 </assert_contents> |
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260 </output> |
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261 <output name="transcripts_combined"> |
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262 <assert_contents> |
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263 <has_n_lines n="18"/> |
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264 </assert_contents> |
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265 </output> |
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266 <output_collection name="tmap_output_collection" type="list" count="2"/> |
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267 </test> |
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268 <!-- Test 02: 2 inputs, no reference, with refsequence, default options (but disable tmap output) --> |
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269 <test expect_num_outputs="4"> |
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270 <param ftype="gtf" name="gffinputs" value="gffcompare_in1.gtf,gffcompare_in2.gtf"/> |
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271 <param name="refmap_tmap" value="false"/> |
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272 <conditional name="conditional_annotation"> |
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273 <param name="selector" value="no"/> |
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274 </conditional> |
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275 <conditional name="seq_data"> |
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276 <param name="selector" value="yes"/> |
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277 <conditional name="seq_source"> |
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278 <param name="index_source" value="history"/> |
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279 <param name="ref_genome" ftype="fasta" value="sequence.fa"/> |
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280 </conditional> |
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281 </conditional> |
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282 <assert_command> |
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283 <not_has_text text="-R "/> |
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284 <not_has_text text="-Q "/> |
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285 <has_text text="-T "/> |
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286 <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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287 <not_has_text text="-M "/> |
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288 <not_has_text text="-N "/> |
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289 <has_text text="-d 100 "/> |
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290 <has_text text="-p 'TCONS' "/> |
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291 <not_has_text text="-C "/> |
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292 <not_has_text text="-A "/> |
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293 <not_has_text text="-X "/> |
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294 <not_has_text text="-K "/> |
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295 </assert_command> |
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296 <output name="transcripts_stats" ftype="txt"> |
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297 <assert_contents> |
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298 <has_line line="#gffcompare -V -T -d 100 -p TCONS gffcompare_in1_gtf gffcompare_in2_gtf"/> |
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299 <has_line line=" Total union super-loci across all input datasets: 7 "/> |
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300 <has_n_lines n="15"/> |
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301 </assert_contents> |
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302 </output> |
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303 <output name="transcripts_loci" ftype="tabular"> |
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304 <assert_contents> |
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305 <has_n_lines n="7"/> |
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306 </assert_contents> |
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307 </output> |
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308 <output name="transcripts_tracking"> |
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309 <assert_contents> |
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310 <has_n_lines n="9"/> |
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311 </assert_contents> |
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312 </output> |
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313 <output name="transcripts_combined"> |
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314 <assert_contents> |
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315 <has_n_lines n="18"/> |
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316 </assert_contents> |
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317 </output> |
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318 </test> |
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319 <!-- Test 03: 2 inputs, no reference, with cached refsequence, default options (but disable tmap output) --> |
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320 <test expect_num_outputs="4"> |
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321 <param ftype="gtf" name="gffinputs" value="gffcompare_in1.gtf,gffcompare_in2.gtf" dbkey="hg17"/> |
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322 <param name="refmap_tmap" value="false"/> |
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323 <conditional name="conditional_annotation"> |
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324 <param name="selector" value="no"/> |
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325 </conditional> |
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326 <conditional name="seq_data"> |
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327 <param name="selector" value="yes"/> |
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328 <conditional name="seq_source"> |
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329 <param name="index_source" value="cached"/> |
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330 <param name="index" value="test_buildid"/> |
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331 </conditional> |
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332 </conditional> |
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333 <assert_command> |
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334 <not_has_text text="-R "/> |
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335 <not_has_text text="-Q "/> |
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336 <has_text text="-T "/> |
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337 <has_text_matching expression="gffcompare.*-s "/> |
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338 <not_has_text text="-M "/> |
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339 <not_has_text text="-N "/> |
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340 <has_text text="-d 100 "/> |
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341 <has_text text="-p 'TCONS' "/> |
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342 <not_has_text text="-C "/> |
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343 <not_has_text text="-A "/> |
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344 <not_has_text text="-X "/> |
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345 <not_has_text text="-K "/> |
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346 </assert_command> |
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347 <output name="transcripts_stats" ftype="txt"> |
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348 <assert_contents> |
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349 <has_line line="#gffcompare -V -T -d 100 -p TCONS gffcompare_in1_gtf gffcompare_in2_gtf"/> |
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350 <has_line line=" Total union super-loci across all input datasets: 7 "/> |
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351 <has_n_lines n="15"/> |
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352 </assert_contents> |
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353 </output> |
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354 <output name="transcripts_loci" ftype="tabular"> |
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355 <assert_contents> |
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356 <has_n_lines n="7"/> |
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357 </assert_contents> |
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358 </output> |
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359 <output name="transcripts_tracking"> |
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360 <assert_contents> |
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361 <has_n_lines n="9"/> |
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362 </assert_contents> |
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363 </output> |
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364 <output name="transcripts_combined"> |
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365 <assert_contents> |
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366 <has_n_lines n="18"/> |
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367 </assert_contents> |
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368 </output> |
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369 </test> |
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370 <!-- Test 04: 2 inputs and reference, default options --> |
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371 <test expect_num_outputs="6"> |
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372 <param ftype="gtf" name="gffinputs" value="gffcompare_in1.gtf,gffcompare_in2.gtf"/> |
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373 <conditional name="conditional_annotation"> |
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374 <param name="selector" value="yes"/> |
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375 <conditional name="ref_source"> |
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376 <param name="ref_source_sel" value="history"/> |
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377 <param ftype="gtf" name="reference_annotation" value="gffcompare_in3.gtf"/> |
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378 </conditional> |
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379 <conditional name="conditional_strict"> |
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380 <param name="selector" value="--strict-match"/> |
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381 <param name="e" value="100"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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diff
changeset
|
382 </conditional> |
|
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
|
383 </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
|
384 <conditional name="seq_data"> |
|
8
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
385 <param name="seletor" value="no"/> |
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1
77c22296fb8e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
parents:
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diff
changeset
|
386 </conditional> |
|
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
|
387 <assert_command> |
|
8
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
388 <not_has_text text="-R "/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
389 <not_has_text text="-Q "/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
390 <has_text text="--strict-match "/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
391 <not_has_text text="-T "/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
392 <not_has_text text="-M "/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
393 <not_has_text text="-N "/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
394 <has_text text="-e 100 "/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
395 <has_text text="-d 100 "/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
396 <not_has_text text="-D "/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
397 <not_has_text text="--no-merge "/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
398 <not_has_text text="--chr-stats"/> |
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3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
399 <has_text text="-p 'TCONS' "/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
400 <not_has_text text="-C "/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
401 <not_has_text text="-A "/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
402 <not_has_text text="-X "/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
403 <not_has_text text="-K "/> |
|
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
|
404 </assert_command> |
|
8
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
405 <output name="transcripts_stats" ftype="txt"> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
406 <assert_contents> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
407 <has_line line=" Total union super-loci across all input datasets: 7 "/> |
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3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
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changeset
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408 <has_line line="#gffcompare -V -r reference_annotation --strict-match -e 100 -d 100 -p TCONS gffcompare_in1_gtf gffcompare_in2_gtf"/> |
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3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
409 </assert_contents> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
410 </output> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
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411 <output name="transcripts_loci" ftype="tabular"> |
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3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
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412 <assert_contents> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
413 <has_n_lines n="7"/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
414 </assert_contents> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
415 </output> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
416 <output name="transcripts_tracking" ftype="tabular"> |
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3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
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417 <assert_contents> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
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418 <has_n_lines n="9"/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
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419 </assert_contents> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
420 </output> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
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421 <output name="transcripts_combined" ftype="gtf"> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
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422 <assert_contents> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
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423 <has_n_lines n="18"/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
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424 </assert_contents> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
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425 </output> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
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426 <output_collection name="refmap_output_collection" type="list" count="2"/> |
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3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
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427 <output_collection name="tmap_output_collection" type="list" count="2"/> |
|
0
e52ca9ad69ca
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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428 </test> |
|
6
9e282a956012
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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429 <!-- Test 05: 2 inputs and reference (cached), non default options --> |
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9e282a956012
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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430 <test expect_num_outputs="6"> |
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8
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
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431 <param ftype="gtf" name="gffinputs" value="gffcompare_in1.gtf,gffcompare_in2.gtf" dbkey="hg17"/> |
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6
9e282a956012
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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432 <conditional name="conditional_annotation"> |
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9e282a956012
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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433 <param name="selector" value="yes"/> |
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3
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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434 <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
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diff
changeset
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435 <param name="ref_source_sel" value="cached"/> |
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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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436 <param name="index" value="test_buildid"/> |
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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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changeset
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437 </conditional> |
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6
9e282a956012
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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438 <param name="R" value="true"/> |
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9e282a956012
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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439 <param name="Q" value="true"/> |
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9e282a956012
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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440 <param name="discard_single_exon" value="-M"/> |
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9e282a956012
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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441 <param name="no_merge" value="true"/> |
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9e282a956012
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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442 <conditional name="conditional_strict"> |
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9e282a956012
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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443 <param name="selector" value="--strict-match"/> |
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9e282a956012
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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444 <param name="e" value="101"/> |
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9e282a956012
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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445 </conditional> |
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9e282a956012
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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446 <conditional name="conditional_duplication"> |
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9e282a956012
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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447 <param name="selector" value="-D"/> |
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9e282a956012
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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448 <param name="S" value="false"/> |
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9e282a956012
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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449 </conditional> |
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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
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450 </conditional> |
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8
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
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451 <param name="max_dist_group" value="99"/> |
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3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
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452 <param name="chr_stats" value="true"/> |
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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
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453 <assert_command> |
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8
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
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454 <has_text text="-R "/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
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455 <has_text text="-Q "/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
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456 <has_text text="--strict-match "/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
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457 <not_has_text text="-T "/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
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458 <has_text text="-M "/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
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459 <not_has_text text="-N "/> |
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3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
7
diff
changeset
|
460 <has_text text="-e 101 "/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
7
diff
changeset
|
461 <has_text text="-d 99 "/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
7
diff
changeset
|
462 <has_text text="-D "/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
7
diff
changeset
|
463 <has_text text="--no-merge "/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
7
diff
changeset
|
464 <has_text text="--chr-stats"/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
465 <has_text text="-p 'TCONS' "/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
7
diff
changeset
|
466 <not_has_text text="-C "/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
7
diff
changeset
|
467 <not_has_text text="-A "/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
7
diff
changeset
|
468 <not_has_text text="-X "/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
7
diff
changeset
|
469 <not_has_text text="-K "/> |
|
3
84845ad0d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
parents:
2
diff
changeset
|
470 </assert_command> |
|
8
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
471 <output name="transcripts_stats" ftype="txt"> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
472 <assert_contents> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
473 <has_line line=" Total union super-loci across all input datasets: 0 "/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
474 <has_line line="#gffcompare -V -r reference_annotation -R -Q --strict-match -e 101 -M -D --no-merge -d 99 --chr-stats -p TCONS gffcompare_in1_gtf gffcompare_in2_gtf"/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
7
diff
changeset
|
475 </assert_contents> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
476 </output> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
7
diff
changeset
|
477 <output name="transcripts_loci" ftype="tabular"> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
7
diff
changeset
|
478 <assert_contents> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
479 <has_n_lines n="0"/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
7
diff
changeset
|
480 </assert_contents> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
7
diff
changeset
|
481 </output> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
7
diff
changeset
|
482 <output name="transcripts_tracking" ftype="tabular"> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
7
diff
changeset
|
483 <assert_contents> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
7
diff
changeset
|
484 <has_n_lines n="0"/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
485 </assert_contents> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
486 </output> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
7
diff
changeset
|
487 <output name="transcripts_combined" ftype="gtf"> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
488 <assert_contents> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
489 <has_n_lines n="0"/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
490 </assert_contents> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
491 </output> |
|
6
9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
5
diff
changeset
|
492 <output_collection name="refmap_output_collection" type="list" count="0"/> <!-- because of -M no refmaps are created --> |
|
9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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diff
changeset
|
493 <output_collection name="tmap_output_collection" type="list" count="2"/> |
|
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
|
494 </test> |
|
6
9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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diff
changeset
|
495 <!-- Test 06: 2 inputs and reference, non default advanced options --> |
|
9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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diff
changeset
|
496 <test expect_num_outputs="6"> |
|
8
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
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diff
changeset
|
497 <param ftype="gtf" name="gffinputs" value="gffcompare_in1.gtf,gffcompare_in2.gtf"/> |
|
6
9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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diff
changeset
|
498 <conditional name="conditional_annotation"> |
|
9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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diff
changeset
|
499 <param name="selector" value="yes"/> |
|
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
|
500 <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
|
501 <param name="ref_source_sel" value="history"/> |
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8
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
502 <param ftype="gtf" name="reference_annotation" value="gffcompare_in3.gtf"/> |
|
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
|
503 </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
|
504 </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
|
505 <conditional name="seq_data"> |
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8
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
506 <param name="selector" value="no"/> |
|
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
|
507 </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
|
508 <section name="adv_output"> |
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8
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
509 <param name="p" value="OTHER"/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
510 <param name="C" value="true"/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
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511 <param name="A" value="true"/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
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diff
changeset
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512 <param name="X" value="true"/> |
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3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
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changeset
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513 <param name="K" value="true"/> |
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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
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514 </section> |
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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
|
515 <assert_command> |
|
8
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
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516 <not_has_text text="-R "/> |
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3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
517 <not_has_text text="-Q "/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
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518 <not_has_text text="--strict-match "/> |
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3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
519 <not_has_text text="-T "/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
520 <not_has_text text="-M "/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
521 <not_has_text text="-N "/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
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522 <not_has_text text="-e 100 "/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
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523 <has_text text="-d 100 "/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
524 <not_has_text text="-D "/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
525 <not_has_text text="--no-merge "/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
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526 <not_has_text text="--chr-stats"/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
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527 <has_text text="-p 'OTHER' "/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
528 <has_text text="-C "/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
529 <has_text text="-A "/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
530 <has_text text="-X "/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
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531 <has_text text="-K "/> |
|
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
|
532 </assert_command> |
|
8
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
533 <output name="transcripts_stats" ftype="txt"> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
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534 <assert_contents> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
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535 <has_line line=" Total union super-loci across all input datasets: 7 "/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
536 <has_line line="#gffcompare -V -r reference_annotation -d 100 -p OTHER -A -C -X -K gffcompare_in1_gtf gffcompare_in2_gtf"/> |
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3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
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diff
changeset
|
537 </assert_contents> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
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diff
changeset
|
538 </output> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
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diff
changeset
|
539 <output name="transcripts_loci" ftype="tabular"> |
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3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
540 <assert_contents> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
541 <has_n_lines n="7"/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
542 </assert_contents> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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changeset
|
543 </output> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
544 <output name="transcripts_tracking" ftype="tabular"> |
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3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
545 <assert_contents> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
546 <has_n_lines n="9"/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
547 </assert_contents> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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changeset
|
548 </output> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
549 <output name="transcripts_combined" ftype="gtf"> |
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3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
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550 <assert_contents> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
551 <has_n_lines n="14"/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
552 </assert_contents> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
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553 </output> |
|
6
9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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diff
changeset
|
554 <output_collection name="tmap_output_collection" type="list" count="2"/> |
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9e282a956012
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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555 <output_collection name="tmap_output_collection" type="list" count="2"/> |
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3
84845ad0d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
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changeset
|
556 </test> |
|
6
9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
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changeset
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557 <!-- Test 07: 2 inputs and reference, default options, no tmap or refmap output --> |
|
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
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558 <test expect_num_outputs="4"> |
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8
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
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parents:
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diff
changeset
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559 <param ftype="gtf" name="gffinputs" value="gffcompare_in1.gtf,gffcompare_in2.gtf"/> |
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6
9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
iuc
parents:
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diff
changeset
|
560 <param name="refmap_tmap" value="false"/> |
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9e282a956012
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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561 <conditional name="conditional_annotation"> |
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9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
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diff
changeset
|
562 <param name="selector" value="yes"/> |
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3
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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563 <conditional name="ref_source"> |
|
84845ad0d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
iuc
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diff
changeset
|
564 <param name="ref_source_sel" value="history"/> |
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8
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
565 <param ftype="gtf" name="reference_annotation" value="gffcompare_in3.gtf"/> |
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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
|
566 </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
|
567 </conditional> |
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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
|
568 <conditional name="seq_data"> |
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8
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
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569 <param name="selector" value="no"/> |
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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
|
570 </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
|
571 <assert_command> |
|
8
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
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572 <not_has_text text="-R "/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
|
573 <not_has_text text="-Q "/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
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574 <not_has_text text="--strict-match "/> |
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3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
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575 <has_text text="-T "/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
parents:
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diff
changeset
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576 <not_has_text text="-M "/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
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changeset
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577 <not_has_text text="-N "/> |
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3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
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578 <has_text text="-d 100 "/> |
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3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
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changeset
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579 <not_has_text text="-D "/> |
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3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
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580 <not_has_text text="--no-merge "/> |
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3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
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changeset
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581 <not_has_text text="--chr-stats"/> |
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3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
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582 <has_text text="-p 'TCONS' "/> |
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3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
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changeset
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583 <not_has_text text="-C "/> |
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3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
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changeset
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584 <not_has_text text="-A "/> |
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3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
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changeset
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585 <not_has_text text="-X "/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
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586 <not_has_text text="-K "/> |
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3
84845ad0d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
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changeset
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587 </assert_command> |
|
8
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
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588 <output name="transcripts_stats" ftype="txt"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
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589 <assert_contents> |
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3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
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590 <has_line line=" Total union super-loci across all input datasets: 7 "/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
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591 <has_line line="#gffcompare -V -r reference_annotation -T -d 100 -p TCONS gffcompare_in1_gtf gffcompare_in2_gtf"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
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592 </assert_contents> |
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3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
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593 </output> |
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3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
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changeset
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594 <output name="transcripts_loci" ftype="tabular"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
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changeset
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595 <assert_contents> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
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changeset
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596 <has_n_lines n="7"/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
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changeset
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597 </assert_contents> |
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3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
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changeset
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598 </output> |
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3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
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changeset
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599 <output name="transcripts_tracking" ftype="tabular"> |
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3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
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changeset
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600 <assert_contents> |
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3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
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changeset
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601 <has_n_lines n="9"/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
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changeset
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602 </assert_contents> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
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changeset
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603 </output> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
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changeset
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604 <output name="transcripts_combined" ftype="gtf"> |
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3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
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changeset
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605 <assert_contents> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
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diff
changeset
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606 <has_n_lines n="18"/> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
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changeset
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607 </assert_contents> |
|
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
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changeset
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608 </output> |
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3
84845ad0d35c
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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609 </test> |
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6
9e282a956012
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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610 <!-- Test 08: 1 inputs and reference, default options, no tmap or refmap output --> |
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1
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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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changeset
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611 <test expect_num_outputs="4"> |
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8
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
iuc
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diff
changeset
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612 <param ftype="gtf" name="gffinputs" value="gffcompare_in4.gtf"/> |
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6
9e282a956012
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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613 <param name="refmap_tmap" value="false"/> |
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9e282a956012
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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614 <conditional name="conditional_annotation"> |
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9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
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changeset
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615 <param name="selector" value="yes"/> |
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3
84845ad0d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
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changeset
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616 <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
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changeset
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617 <param name="ref_source_sel" value="history"/> |
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8
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
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618 <param ftype="gtf" name="reference_annotation" value="gffcompare_in5.gtf"/> |
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3
84845ad0d35c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
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changeset
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619 </conditional> |
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6
9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
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changeset
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620 <param name="R" value="true"/> |
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9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
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changeset
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621 <param name="Q" value="false"/> |
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9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
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changeset
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622 <conditional name="conditional_strict"> |
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9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
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changeset
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623 <param name="selector" value="--strict-match"/> |
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9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
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changeset
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624 <param name="e" value="100"/> |
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9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
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changeset
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625 </conditional> |
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9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
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626 <param name="discard_single_exon" value=""/> |
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1
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit fc3616bd1463afef9681cd7c431ac29f79e37e74
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627 </conditional> |
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8
3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
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628 <param name="max_dist_group" value="100"/> |
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3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
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changeset
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629 <output name="transcripts_stats" ftype="txt"> |
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3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
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630 <assert_contents> |
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3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
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631 <has_line line=" Total union super-loci across all input datasets: 29 "/> |
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3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
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632 <has_line line="#gffcompare -V -r reference_annotation -R --strict-match -e 100 -T -d 100 -p TCONS gffcompare_in4_gtf"/> |
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3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
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633 </assert_contents> |
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3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
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634 </output> |
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3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
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635 <output name="transcripts_loci" ftype="tabular"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
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636 <assert_contents> |
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3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
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637 <has_n_lines n="29"/> |
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3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
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638 </assert_contents> |
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3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
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639 </output> |
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3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
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640 <output name="transcripts_tracking" ftype="tabular"> |
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3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
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641 <assert_contents> |
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3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
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642 <has_n_lines n="35"/> |
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3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
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643 </assert_contents> |
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3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
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644 </output> |
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3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
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645 <output name="transcripts_combined" ftype="tabular"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
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646 <assert_contents> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
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647 <has_n_lines n="35"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
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648 </assert_contents> |
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3b8c94e2674a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c62791a7ff6fef8cb19b84465662d13effaffe1d
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649 </output> |
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0
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650 </test> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
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651 </tests> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
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652 <help> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
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653 <![CDATA[ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
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654 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
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655 .. class:: infomark |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
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656 |
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0
e52ca9ad69ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
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657 **GffCompare Overview** |
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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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658 |
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6
9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
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659 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, |
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9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
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660 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. |
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9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
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661 When multiple transcript files (samples) are provided, GffCompare generates a non-redundant combined set of transcripts, tracking structurally equivalent transcripts across multiple |
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9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
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662 samples and classifying them according to their relationship to reference transcripts. GffCompare has the following main functions: |
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9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
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663 |
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9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
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664 - Merge structurally equivalent transcripts and transcript fragments (transfrags) across multiple samples |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
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665 - Assess the accuracy of the assembled transcripts from an RNA-Seq sample by comparing it to known annotation |
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9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
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666 - Track, annotate, and report all structurally distinct transfrags across multiple samples |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
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667 |
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9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
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668 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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9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
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669 reference transcript that they most closely overlap. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
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670 |
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9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
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671 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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9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
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672 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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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
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673 |
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9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
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674 ---- |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
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675 |
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9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
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676 .. class:: infomark |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
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677 |
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9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
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678 **Annotation mode** |
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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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679 |
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6
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
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680 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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9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
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681 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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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
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682 |
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9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
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683 ---- |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
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684 |
|
9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
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changeset
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685 .. class:: infomark |
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9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
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686 |
|
9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
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687 **Merging structually equivalent transcripts** |
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9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
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688 |
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9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
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689 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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9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
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690 exact intron chain is present in both samples, it is thus reported only once in the output 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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changeset
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691 |
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9e282a956012
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
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692 **The "super-locus" concept** |
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693 |
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694 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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695 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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696 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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697 |
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698 ---- |
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699 |
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700 .. class:: infomark |
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702 **Transcript accuracy estimation** |
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703 |
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704 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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705 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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706 |
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707 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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708 |
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709 * Sensitivity = TP/(TP+FN) |
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710 * Precision = TP/(TP+FP) |
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711 |
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712 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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713 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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714 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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715 for each sample. |
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716 |
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717 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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718 when compared to the reference annotation. The six different levels that GffCompare uses are described below: |
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719 |
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720 * **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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721 * **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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722 * **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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723 * **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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724 * **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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725 * **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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726 |
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727 ---- |
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729 .. class:: infomark |
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730 |
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731 **Tracking transcripts** |
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732 |
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733 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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734 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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735 |
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736 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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737 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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738 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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739 transcript from each input file in order. |
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740 |
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741 **RefMap and TMAP files** |
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742 |
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743 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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744 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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745 file describe the most closely matching reference transcript for that transcript. |
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746 |
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747 ]]> |
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748 </help> |
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749 <expand macro="citations"/> |
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750 </tool> |