Mercurial > repos > iuc > gffcompare

comparison gffcompare.xml @ 1:77c22296fb8e 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/tools/gffcompare commit fc3616bd1463afef9681cd7c431ac29f79e37e74
author iuc
date Wed, 12 Dec 2018 03:18:21 -0500
parents e52ca9ad69ca
children 66f066ca5d60
comparison
equal deleted inserted replaced
0:e52ca9ad69ca 1:77c22296fb8e
1 <tool id="gffcompare" name="GffCompare" version="0.9.8"> 1 <tool id="gffcompare" name="GffCompare" version="0.9.8+galaxy1">
2 <description>compare assembled transcripts to a reference annotation</description> 2 <description>compare assembled transcripts to a reference annotation</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.9.8">gffcompare</requirement> 4 <requirement type="package" version="0.9.8">gffcompare</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <stdio>
8 <exit_code range=":-1" /> 8 <exit_code range=":-1" />
9 <regex match="Error" /> 9 <regex match="Error" />
10 <regex match="Exception" /> 10 <regex match="Exception" />
11 </stdio> 11 </stdio>
12 <version_command>gffcompare -v | awk '{print $2}'</version_command> 12 <version_command>gffcompare -v | awk '{print $2}'</version_command>
13 <command> 13 <command><![CDATA[
14 <![CDATA[ 14 #import re
15 #set $input_gtf = "' '".join(str($inputs).split(',')) 15 #set escaped_element_identifiers = [re.sub('[^\w\-]', '_', str(_.element_identifier)) for _ in $gffinputs]
16 #if $seq_data.use_seq_data == "Yes": 16 #for $input, $escaped_element_identifier in zip($gffinputs, $escaped_element_identifiers):
17 #if $seq_data.seq_source.index_source == "history": 17 ln -s '$input' '$escaped_element_identifier' &&
18 ln -s '$seq_data.seq_source.ref_file' ref_seq.fa && 18 #end for
19 #else: 19 #if $seq_data.use_seq_data == "Yes":
20 ln -s '${seq_data.seq_source.index.fields.path}' ref_seq.fa && 20 #if $seq_data.seq_source.index_source == "history":
21 #end if 21 ln -s '$seq_data.seq_source.ref_file' ref_seq.fa &&
22 #end if 22 #else:
23 gffcompare 23 ln -s '${seq_data.seq_source.index.fields.path}' ref_seq.fa &&
24 ## Use annotation reference? 24 #end if
25 #if $annotation.use_ref_annotation == "Yes": 25 #end if
26 -r '$annotation.reference_annotation' $annotation.ignore_nonoverlapping_reference $annotation.ignore_nonoverlapping_transfrags 26
27 #end if 27 gffcompare
28 28 ## Use annotation reference?
29 ## Use sequence data? 29 #if $annotation.use_ref_annotation == "Yes":
30 30 -r '$annotation.reference_annotation'
31 #if $seq_data.use_seq_data == "Yes": 31 $annotation.ignore_nonoverlapping_reference
32 -s ref_seq.fa 32 $annotation.ignore_nonoverlapping_transfrags
33 #end if 33 #if not $annotation.refmap_tmap:
34 34 -T
35 $discard_single_exon -e $max_dist_exon -d $max_dist_group $discard_intron_redundant_transfrags 35 #end if
36 36 #end if
37 '$input_gtf' 37
38 ]]> 38 ## Use sequence data?
39 </command> 39 #if $seq_data.use_seq_data == "Yes":
40 -s ref_seq.fa
41 #end if
42
43 $discard_single_exon
44 -e $max_dist_exon
45 -d $max_dist_group
46 $discard_intron_redundant_transfrags
47
48 #for $escaped_element_identifier in $escaped_element_identifiers:
49 '$escaped_element_identifier'
50 #end for
51 ]]></command>
40 <inputs> 52 <inputs>
41 <param format="gtf" name="inputs" type="data" label="GTF inputs for comparison" help="" multiple="true" /> 53 <param format="gtf" name="gffinputs" type="data" label="GTF inputs for comparison" help="" multiple="true" />
42 <conditional name="annotation"> 54 <conditional name="annotation">
43 <param label="Use Reference Annotation" name="use_ref_annotation" type="select"> 55 <param label="Use Reference Annotation" name="use_ref_annotation" type="select">
44 <option value="No">No</option> 56 <option value="No">No</option>
45 <option value="Yes">Yes</option> 57 <option value="Yes">Yes</option>
46 </param> 58 </param>
47 <when value="Yes"> 59 <when value="Yes">
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" /> 60 <param argument="-r" format="gff3,gtf" help="Requires an annotation file in GFF3 or GTF format." label="Reference Annotation" name="reference_annotation" type="data" />
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" /> 61 <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" />
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" /> 62 <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" />
63 <param argument="-T" name="refmap_tmap" label="Generate tmap and refmap files for each input file" type="select" multiple="True">
64 <option value="refmap" selected="True">refmap</option>
65 <option value="tmap" selected="True">tmap</option>
66 </param>
51 </when> 67 </when>
52 <when value="No"> 68 <when value="No">
53 </when> 69 </when>
54 </conditional> 70 </conditional>
55 <conditional name="seq_data"> 71 <conditional name="seq_data">
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"> 72 <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">
57 <option value="Yes">Yes</option> 73 <option value="Yes">Yes</option>
58 <option value="No">No</option> 74 <option value="No">No</option>
59 </param> 75 </param>
60 <when value="No" /> 76 <when value="No"/>
61 <when value="Yes"> 77 <when value="Yes">
62 <conditional name="seq_source"> 78 <conditional name="seq_source">
63 <param label="Choose the source for the reference list" name="index_source" type="select"> 79 <param label="Choose the source for the reference list" name="index_source" type="select">
64 <option value="cached">Locally cached</option> 80 <option value="cached">Locally cached</option>
65 <option value="history">History</option> 81 <option value="history">History</option>
66 </param> 82 </param>
67 <when value="cached"> 83 <when value="cached">
68 <param argument="-s" label="Using reference genome" name="index" type="select"> 84 <param argument="-s" label="Using reference genome" name="index" type="select">
69 <options from_data_table="fasta_indexes"> 85 <options from_data_table="fasta_indexes">
70 <filter column="1" key="dbkey" ref="inputs" type="data_meta" /> 86 <filter column="1" key="dbkey" ref="gffinputs" type="data_meta" />
71 <validator message="No reference genome is available for the build associated with the selected input dataset" type="no_options" /> 87 <validator message="No reference genome is available for the build associated with the selected input dataset" type="no_options" />
72 </options> 88 </options>
73 </param> 89 </param>
74 </when> 90 </when>
75 <when value="history"> 91 <when value="history">
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" /> 104 <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" />
89 </inputs> 105 </inputs>
90 <outputs> 106 <outputs>
91 <data format="txt" from_work_dir="gffcmp.stats" label="${tool.name} on ${on_string}: transcript accuracy" name="transcripts_stats" /> 107 <data format="txt" from_work_dir="gffcmp.stats" label="${tool.name} on ${on_string}: transcript accuracy" name="transcripts_stats" />
92 <data format="tabular" from_work_dir="gffcmp.loci" label="${tool.name} on ${on_string}: loci" name="transcripts_loci" /> 108 <data format="tabular" from_work_dir="gffcmp.loci" label="${tool.name} on ${on_string}: loci" name="transcripts_loci" />
93 <data format="tabular" from_work_dir="gffcmp.tracking" label="${tool.name} on ${on_string}: data ${inputs[0].hid} tracking file" name="transcripts_tracking" /> 109 <data format="tabular" from_work_dir="gffcmp.tracking" label="${tool.name} on ${on_string}: data ${gffinputs[0].hid} tracking file" name="transcripts_tracking" />
94 <data format="gtf" from_work_dir="gffcmp.combined.gtf" label="${tool.name} on ${on_string}: combined transcripts" name="transcripts_combined"> 110 <data format="gtf" from_work_dir="gffcmp.combined.gtf" label="${tool.name} on ${on_string}: combined transcripts" name="transcripts_combined">
95 <filter>(use_seq_data == 'No')</filter> 111 <filter>isinstance(gffinputs, list)</filter>
96 </data> 112 </data>
97 <data format="gtf" from_work_dir="gffcmp.annotated.gtf" label="${tool.name} on ${on_string}: annotated transcripts" name="transcripts_annotated"> 113 <data format="gtf" from_work_dir="gffcmp.annotated.gtf" label="${tool.name} on ${on_string}: annotated transcripts" name="transcripts_annotated">
98 <filter>(use_seq_data == 'Yes')</filter> 114 <filter>not isinstance(gffinputs, list)</filter>
99 </data> 115 </data>
116 <collection name="refmap_output" type="list" label="${tool.name} on ${on_string}: refmap">
117 <discover_datasets pattern="gffcmp\.(?P&lt;designation&gt;.+)\.refmap" ext="tabular" />
118 <filter>annotation['use_ref_annotation'] == 'Yes' and annotation['refmap_tmap'] != None and 'refmap' in annotation['refmap_tmap']</filter>
119 </collection>
120 <collection name="tmap_output" type="list" label="${tool.name} on ${on_string}: tmap">
121 <discover_datasets pattern="gffcmp\.(?P&lt;designation&gt;.+)\.tmap" ext="tabular" />
122 <filter>annotation['use_ref_annotation'] == 'Yes' and annotation['refmap_tmap'] != None and 'tmap' in annotation['refmap_tmap']</filter>
123 </collection>
100 </outputs> 124 </outputs>
101 <tests> 125 <tests>
102 <test> 126 <test expect_num_outputs="6">
103 <param ftype="gtf" name="inputs" value="gffcompare_in1.gtf,gffcompare_in2.gtf" /> 127 <param ftype="gtf" name="gffinputs" value="gffcompare_in1.gtf,gffcompare_in2.gtf" />
104 <param name="use_ref_annotation" value="Yes" /> 128 <param name="use_ref_annotation" value="Yes" />
105 <param ftype="gtf" name="reference_annotation" value="gffcompare_in3.gtf" /> 129 <conditional name="annotation">
106 <param name="ignore_nonoverlapping_reference" value="Yes" /> 130 <param ftype="gtf" name="reference_annotation" value="gffcompare_in3.gtf" />
107 <param name="ignore_nonoverlapping_transfrags" value="No" /> 131 <param name="ignore_nonoverlapping_reference" value="Yes" />
132 <param name="ignore_nonoverlapping_transfrags" value="No" />
133 </conditional>
108 <param name="use_seq_data" value="No" /> 134 <param name="use_seq_data" value="No" />
109 <param name="discard_single_exon" value="" /> 135 <param name="discard_single_exon" value="" />
110 <param name="max_dist_exon" value="100" /> 136 <param name="max_dist_exon" value="100" />
111 <param name="max_dist_group" value="100" /> 137 <param name="max_dist_group" value="100" />
112 <param name="discard_intron_redundant_transfrags" value="No" /> 138 <param name="discard_intron_redundant_transfrags" value="No" />
113 <output file="gffcompare_out1.stats" name="transcripts_stats" lines_diff="6" /> 139 <output file="gffcompare_out1.stats" name="transcripts_stats" lines_diff="6" />
114 <output file="gffcompare_out1.loci" name="transcripts_loci" /> 140 <output file="gffcompare_out1.loci" name="transcripts_loci" lines_diff="2" />
115 <output file="gffcompare_out1.tracking" name="transcripts_tracking" /> 141 <output file="gffcompare_out1.tracking" name="transcripts_tracking" />
116 <output file="gffcompare_out1.gtf" name="transcripts_combined" /> 142 <output file="gffcompare_out1.gtf" name="transcripts_combined" />
143 <output_collection name="refmap_output" type="list" count="2">
144 <element name="gffcompare_in1_gtf" file="gffcompare_out1-1.refmap" ftype="tabular" />
145 <element name="gffcompare_in2_gtf" file="gffcompare_out1-2.refmap" ftype="tabular" />
146 </output_collection>
147 <output_collection name="tmap_output" type="list" count="2">
148 <element name="gffcompare_in1_gtf" file="gffcompare_out1-1.tmap" ftype="tabular" />
149 <element name="gffcompare_in2_gtf" file="gffcompare_out1-2.tmap" ftype="tabular" />
150 </output_collection>
117 </test> 151 </test>
118 <test> 152 <test expect_num_outputs="4">
119 <param ftype="gtf" name="inputs" value="gffcompare_in4.gtf" /> 153 <param ftype="gtf" name="gffinputs" value="gffcompare_in4.gtf" />
120 <param name="use_ref_annotation" value="Yes" /> 154 <param name="use_ref_annotation" value="Yes" />
121 <param ftype="gtf" name="reference_annotation" value="gffcompare_in5.gtf" /> 155 <conditional name="annotation">
122 <param name="ignore_nonoverlapping_reference" value="Yes" /> 156 <param ftype="gtf" name="reference_annotation" value="gffcompare_in5.gtf" />
123 <param name="ignore_nonoverlapping_transfrags" value="No" /> 157 <param name="ignore_nonoverlapping_reference" value="Yes" />
158 <param name="ignore_nonoverlapping_transfrags" value="No" />
159 <param name="refmap_tmap" value="" />
160 </conditional>
124 <param name="use_seq_data" value="No" /> 161 <param name="use_seq_data" value="No" />
125 <param name="discard_single_exon" value="" /> 162 <param name="discard_single_exon" value="" />
126 <param name="max_dist_exon" value="100" /> 163 <param name="max_dist_exon" value="100" />
127 <param name="max_dist_group" value="100" /> 164 <param name="max_dist_group" value="100" />
128 <param name="discard_intron_redundant_transfrags" value="No" /> 165 <param name="discard_intron_redundant_transfrags" value="No" />
129 <output file="gffcompare_out2.stats" name="transcripts_stats" lines_diff="6" /> 166 <output file="gffcompare_out2.stats" name="transcripts_stats" lines_diff="6" />
130 <output file="gffcompare_out2.loci" name="transcripts_loci" lines_diff="2" /> 167 <output file="gffcompare_out2.loci" name="transcripts_loci" />
131 <output file="gffcompare_out2.tracking" name="transcripts_tracking" /> 168 <output file="gffcompare_out2.tracking" name="transcripts_tracking" />
132 <output file="gffcompare_out2.gtf" name="transcripts_annotated" /> 169 <output file="gffcompare_out2.gtf" name="transcripts_annotated" />
133 </test> 170 </test>
134 </tests> 171 </tests>
135 <help> 172 <help>