Mercurial > repos > iuc > gffcompare

annotate gffcompare.xml @ 0:3c97c841a443 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
author iuc
date Fri, 07 Apr 2017 16:02:07 -0400
parents
children c80cdc2eac6d
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
1 <tool id="gffcompare" name="GffCompare" version="0.9.8">
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
2 <description>compare assembled transcripts to a reference annotation</description>
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
3 <requirements>
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
4 <requirement type="package" version="0.9.8">gffcompare</requirement>
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
5 </requirements>
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
6 <stdio>
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
7 <exit_code range="1:" />
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
8 <exit_code range=":-1" />
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
9 <regex match="Error" />
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
10 <regex match="Exception" />
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
11 </stdio>
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
12 <version_command>gffcompare -v | awk '{print $2}'</version_command>
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
13 <command>
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
14 <![CDATA[
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
15 #set $input_gtf = "' '".join(str($inputs).split(','))
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
16 #if $seq_data.use_seq_data == "Yes":
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
17 #if $seq_data.seq_source.index_source == "history":
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
18 ln -s '$seq_data.seq_source.ref_file' ref_seq.fa &&
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
19 #else:
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
20 ln -s '${seq_data.seq_source.index.fields.path}' ref_seq.fa &&
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
21 #end if
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
22 #end if
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
23 gffcompare
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
24 ## Use annotation reference?
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
25 #if $annotation.use_ref_annotation == "Yes":
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
26 -r '$annotation.reference_annotation' $annotation.ignore_nonoverlapping_reference $annotation.ignore_nonoverlapping_transfrags
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
27 #end if
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
28
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
29 ## Use sequence data?
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
30
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
31 #if $seq_data.use_seq_data == "Yes":
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
32 -s ref_seq.fa
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
33 #end if
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
34
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
35 $discard_single_exon -e $max_dist_exon -d $max_dist_group $discard_intron_redundant_transfrags
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
36
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
37 '$input_gtf'
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
38 ]]>
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
39 </command>
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
40 <inputs>
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
41 <param format="gtf" name="inputs" type="data" label="GTF inputs for comparison" help="" multiple="true" />
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
42 <conditional name="annotation">
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
43 <param label="Use Reference Annotation" name="use_ref_annotation" type="select">
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
44 <option value="No">No</option>
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
45 <option value="Yes">Yes</option>
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
46 </param>
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
47 <when value="Yes">
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
48 <param argument="-r" format="gff3,gtf" help="Requires an annotation file in GFF3 or GTF format." label="Reference Annotation" name="reference_annotation" type="data" />
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
49 <param argument="-R" falsevalue="" help="consider only the reference transcripts that overlap any of the input transfrags (Sn correction)" label="Ignore reference transcripts that are not overlapped by any input transfrags" name="ignore_nonoverlapping_reference" truevalue="-R" type="boolean" />
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
50 <param argument="-Q" falsevalue="" help="consider only the input transcripts that overlap any of the reference transcripts (Sp correction). Warning: this will discard all 'novel' loci!" label="Ignore input transcripts that are not overlapped by any reference transcripts" name="ignore_nonoverlapping_transfrags" truevalue="-Q" type="boolean" />
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
51 </when>
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
52 <when value="No">
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
53 </when>
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
54 </conditional>
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
55 <conditional name="seq_data">
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
56 <param help="Use sequence data for some optional classification functions, including the addition of the p_id attribute required by Cuffdiff." label="Use Sequence Data" name="use_seq_data" type="select">
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
57 <option value="Yes">Yes</option>
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
58 <option value="No">No</option>
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
59 </param>
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
60 <when value="No" />
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
61 <when value="Yes">
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
62 <conditional name="seq_source">
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
63 <param label="Choose the source for the reference list" name="index_source" type="select">
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
64 <option value="cached">Locally cached</option>
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
65 <option value="history">History</option>
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
66 </param>
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
67 <when value="cached">
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
68 <param argument="-s" label="Using reference genome" name="index" type="select">
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
69 <options from_data_table="fasta_indexes">
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
70 <filter column="1" key="dbkey" ref="inputs" type="data_meta" />
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
71 <validator message="No reference genome is available for the build associated with the selected input dataset" type="no_options" />
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
72 </options>
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
73 </param>
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
74 </when>
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
75 <when value="history">
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
76 <param argument="-s" format="fasta" label="Using reference file" name="ref_file" type="data" />
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
77 </when>
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
78 </conditional>
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
79 </when>
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
80 </conditional>
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
81 <param argument="-M/-N" label="discard (ignore) single-exon transcripts" name="discard_single_exon" type="select">
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
82 <option selected="True" value="">No</option>
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
83 <option value="-M">Discard single-exon transfrags and reference transcripts</option>
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
84 <option value="-N">Discard single-exon reference transcripts</option>
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
85 </param>
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
86 <param argument="-e" help="max. distance (range) allowed from free ends of terminal exons of reference transcripts when assessing exon accuracy. Default: 100" label="Max. Distance for assessing exon accuracy" name="max_dist_exon" type="integer" value="100" />
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
87 <param argument="-d" help="max. distance (range) for grouping transcript start sites. Default: 100" label="Max distance for transcript grouping" name="max_dist_group" type="integer" value="100" />
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
88 <param argument="-F" help="Discard intron-redundant transfrags if they share the 5' end (if they differ only at the 3' end)" truevalue="-F" falsevalue="" label="discard intron-redundant transfrags sharing 5'" name="discard_intron_redundant_transfrags" type="boolean" />
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
89 </inputs>
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
90 <outputs>
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
91 <data format="txt" from_work_dir="gffcmp.stats" label="${tool.name} on ${on_string}: transcript accuracy" name="transcripts_stats" />
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
92 <data format="tabular" from_work_dir="gffcmp.loci" label="${tool.name} on ${on_string}: loci" name="transcripts_loci" />
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
93 <data format="tabular" from_work_dir="gffcmp.tracking" label="${tool.name} on ${on_string}: data ${inputs[0].hid} tracking file" name="transcripts_tracking" />
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
94 <data format="gtf" from_work_dir="gffcmp.combined.gtf" label="${tool.name} on ${on_string}: combined transcripts" name="transcripts_combined">
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
95 <filter>(use_seq_data == 'No')</filter>
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
96 </data>
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
97 <data format="gtf" from_work_dir="gffcmp.annotated.gtf" label="${tool.name} on ${on_string}: annotated transcripts" name="transcripts_annotated">
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
98 <filter>(use_seq_data == 'Yes')</filter>
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
99 </data>
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
100 </outputs>
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
101 <tests>
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
102 <test>
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
103 <param ftype="gtf" name="inputs" value="gffcompare_in1.gtf,gffcompare_in2.gtf" />
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
104 <param name="use_ref_annotation" value="Yes" />
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
105 <param ftype="gtf" name="reference_annotation" value="gffcompare_in3.gtf" />
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
106 <param name="ignore_nonoverlapping_reference" value="Yes" />
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
107 <param name="ignore_nonoverlapping_transfrags" value="No" />
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
108 <param name="use_seq_data" value="No" />
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
109 <param name="discard_single_exon" value="" />
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
110 <param name="max_dist_exon" value="100" />
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
111 <param name="max_dist_group" value="100" />
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
112 <param name="discard_intron_redundant_transfrags" value="No" />
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
113 <output file="gffcompare_out1.stats" name="transcripts_stats" lines_diff="6" />
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
114 <output file="gffcompare_out1.loci" name="transcripts_loci" />
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
115 <output file="gffcompare_out1.tracking" name="transcripts_tracking" />
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
116 <output file="gffcompare_out1.gtf" name="transcripts_combined" />
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
117 </test>
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
118 <test>
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
119 <param ftype="gtf" name="inputs" value="gffcompare_in4.gtf" />
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
120 <param name="use_ref_annotation" value="Yes" />
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
121 <param ftype="gtf" name="reference_annotation" value="gffcompare_in5.gtf" />
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
122 <param name="ignore_nonoverlapping_reference" value="Yes" />
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
123 <param name="ignore_nonoverlapping_transfrags" value="No" />
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
124 <param name="use_seq_data" value="No" />
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
125 <param name="discard_single_exon" value="" />
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
126 <param name="max_dist_exon" value="100" />
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
127 <param name="max_dist_group" value="100" />
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
128 <param name="discard_intron_redundant_transfrags" value="No" />
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
129 <output file="gffcompare_out2.stats" name="transcripts_stats" lines_diff="6" />
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
130 <output file="gffcompare_out2.loci" name="transcripts_loci" lines_diff="2" />
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
131 <output file="gffcompare_out2.tracking" name="transcripts_tracking" />
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
132 <output file="gffcompare_out2.gtf" name="transcripts_annotated" />
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
133 </test>
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
134 </tests>
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
135 <help>
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
136 <![CDATA[
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
137 **GffCompare Overview**
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
138
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
139 ## GffCompare
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
140 * compare and evaluate the accuracy of RNA-Seq transcript assemblers (Cufflinks, Stringtie).
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
141 * collapse (merge) duplicate transcripts from multiple GTF/GFF3 files (e.g. resulted from assembly of different samples)
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
142 * classify transcripts from one or multiple GTF/GFF3 files as they relate to reference transcripts provided in a
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
143 annotation file (also in GTF/GFF3 format)
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
144
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
145 The original form of this program is also distributed as part of the Cufflinks suite, under the name "CuffCompare"
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
146 (see manual: http://cole-trapnell-lab.github.io/cufflinks/cuffcompare/). Most of the options and parameters of CuffCompare
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
147 are supported by GffCompare, while new features will likely be added to GffCompare in the future.
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
148
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
149 A notable difference from GffCompare is that when a single query GTF/GFF file is given as input, along with a reference annotation (-r option),
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
150 gffcompare switches into "annotation mode" and it generates a .annotated.gtf file instead of the .merged.gtf produced by CuffCompare with the
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
151 same parameters. This file has the same general format as CuffCompare's .merged.gtf file (with "class codes" assigned to transcripts as per
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
152 their relationship with the matching/overlapping reference transcript), but the original transcript IDs are preserved, so gffcompare can thus
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
153 be used as a simple way of annotating a set of transcripts.
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
154
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
155 Another important difference is that the input transcripts are no longer discarded when they are found to be "intron redundant", i.e.
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
156 contained within other, longer isoforms. CuffCompare had the -G option to prevent collapsing of such intron redundant isoforms into
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
157 their longer "containers", but GffCompare has made this the default mode of operation (hence the -G option is no longer needed
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
158 and is simply ignored when given).
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
159 ]]>
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
160 </help>
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
161 <citations>
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
162 <citation type="doi">10.1038/nbt.1621</citation>
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
163 </citations>
3c97c841a443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a
iuc
parents:
diff changeset
164 </tool>