Mercurial > repos > iuc > gffcompare
comparison gffcompare.xml @ 1:c80cdc2eac6d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit fc3616bd1463afef9681cd7c431ac29f79e37e74
author | iuc |
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date | Wed, 12 Dec 2018 03:19:14 -0500 |
parents | 3c97c841a443 |
children | f99d7825a501 |
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0:3c97c841a443 | 1:c80cdc2eac6d |
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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 ${on_string}: refmap"> | |
117 <discover_datasets pattern="gffcmp\.(?P<designation>.+)\.refmap" ext="tabular" /> | |
118 <filter>annotation['use_ref_annotation'] == 'Yes' and annotation['refmap_tmap'] != None and 'refmap' in annotation['refmap_tmap']</filter> | |
119 </collection> | |
120 <collection name="tmap_output" type="list" label="${tool.name} on ${on_string}: tmap"> | |
121 <discover_datasets pattern="gffcmp\.(?P<designation>.+)\.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> |