Mercurial > repos > iracooke > protk_proteogenomics

annotate protxml_to_gff.xml @ 3:86fd1757f102 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 864b3f087fff3a7cb18b2c0dd61442c2495e5b98
author iracooke
date Mon, 21 Dec 2015 23:43:55 -0500
parents 68d8c9e521d7
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
28067ed4ea0e Docker support and update for protk 1.4
iracooke
parents:
diff changeset
1 <tool id="protxml_to_gff" name="Proteomics to GFF" version="1.1.0">
2
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
2 <description>Export Proteomics Data to GFF</description>
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
3 <requirements>
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
4 <container type="docker">iracooke/protk-1.4.3</container>
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
5 <requirement type="package" version="1.4.3">protk</requirement>
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
6 <requirement type="package" version="2.2.29">blast+</requirement>
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
7 </requirements>
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
8 <stdio>
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
9 <exit_code range="1:" level="fatal" description="Failure" />
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
10 </stdio>
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
11 <command>
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
12 protxml_to_gff.rb $protxml_file
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
13 #if $database.source_select=="built_in":
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
14 -d $database.dbkey
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
15 #else
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
16 -d $database.fasta_file
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
17 #end if
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
18 -c $gene_file
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
19 #if str( $gffidpattern ):
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
20 --gff-idregex='$gffidpattern'
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
21 #end if
0
28067ed4ea0e Docker support and update for protk 1.4
iracooke
parents:
diff changeset
22
2
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
23 #if str( $genomeidpattern ):
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
24 --genome-idregex='$genomeidpattern'
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
25 #end if
0
28067ed4ea0e Docker support and update for protk 1.4
iracooke
parents:
diff changeset
26
2
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
27 #if str( $ignorepattern ):
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
28 --ignore-regex='$ignorepattern'
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
29 #end if
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
30
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
31 --threshold=$peptide_threshold
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
32 --prot-threshold=$prot_threshold
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
33 $stack_charges
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
34 -o $output
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
35 </command>
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
36 <inputs>
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
37 <conditional name="database">
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
38 <param name="source_select" type="select" label="Database source used for Proteomics Searches" help="Database should be an amino acid fasta file with entry id's that can be parsed to obtain contig or scaffold ids referenced in your gff file">
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
39 <option value="input_ref">Your Upload File</option>
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
40 <option value="built_in">Built-In</option>
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
41 </param>
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
42 <when value="built_in">
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
43 <param name="dbkey" type="select" format="text" >
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
44 <label>Database</label>
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
45 <options from_file="pepxml_databases.loc">
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
46 <column name="name" index="0" />
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
47 <column name="value" index="2" />
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
48 </options>
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
49 </param>
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
50 </when>
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
51 <when value="input_ref">
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
52 <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
53 </when>
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
54 </conditional>
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
55 <param name="protxml_file" type="data" format="protxml" multiple="false" label="Proteomics Search Results" help="A ProtXML file produced by Protein Prophet"/>
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
56 <param name="gene_file" type="data" format="gff3" multiple="false" label="Protein coordinates" help="A gff3 file with coordinates for all protein entries used for proteomics searches. Coordinates should correspond to entries in the genome fasta file"/>
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
57 <param name="peptide_threshold" label="Peptide Probability Threshold" type="float" value="0.95" min="0" max="1" help="Only peptides within accepted proteins and passing this threshold will appear in the output"/>
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
58 <param name="prot_threshold" label="Protein Probability Threshold" type="float" value="0.99" min="0" max="1" help="Only peptides within proteins passing this threshold will appear in the output"/>
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
59 <param name="stack_charges" value="false" type="boolean" label="Peptides with different charges get separate gff entries" help="" truevalue="--stack-charge-states" falsevalue="" />
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
60 <param name="gffidpattern" size="40" type="text" value="lcl\|([^ ]*)" label="gff id regex" help="Regex with capture group for parsing gff ids from protein ids">
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
61 <sanitizer>
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
62 <valid initial="string.printable">
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
63 <remove value="&apos;"/>
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
64 </valid>
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
65 <mapping initial="none">
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
66 <add source="&apos;" target="__sq__"/>
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
67 </mapping>
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
68 </sanitizer>
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
69 </param>
0
28067ed4ea0e Docker support and update for protk 1.4
iracooke
parents:
diff changeset
70
2
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
71 <param name="genomeidpattern" size="40" type="text" label="genome id regex" help="Regex with capture group for parsing genomic ids from protein ids">
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
72 <sanitizer>
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
73 <valid initial="string.printable">
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
74 <remove value="&apos;"/>
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
75 </valid>
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
76 <mapping initial="none">
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
77 <add source="&apos;" target="__sq__"/>
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
78 </mapping>
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
79 </sanitizer>
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
80 </param>
0
28067ed4ea0e Docker support and update for protk 1.4
iracooke
parents:
diff changeset
81
2
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
82 <param name="ignorepattern" size="40" type="text" label="ignore regex" help="Regex to match protein ids that we should ignore completely">
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
83 <sanitizer>
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
84 <valid initial="string.printable">
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
85 <remove value="&apos;"/>
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
86 </valid>
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
87 <mapping initial="none">
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
88 <add source="&apos;" target="__sq__"/>
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
89 </mapping>
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
90 </sanitizer>
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
91 </param>
0
28067ed4ea0e Docker support and update for protk 1.4
iracooke
parents:
diff changeset
92
28067ed4ea0e Docker support and update for protk 1.4
iracooke
parents:
diff changeset
93
28067ed4ea0e Docker support and update for protk 1.4
iracooke
parents:
diff changeset
94
2
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
95 </inputs>
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
96 <outputs>
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
97 <data format="gff3" name="output" />
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
98 </outputs>
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
99 <tests>
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
100 <test>
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
101 <param name="source_select" value="input_ref"/>
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
102 <param name="fasta_file" value="small_prot.fasta" format="fasta"/>
0
28067ed4ea0e Docker support and update for protk 1.4
iracooke
parents:
diff changeset
103
2
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
104 <param name="protxml_file" value="small.prot.xml" format="protxml"/>
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
105 <param name="gene_file" value="small_combined.gff" format="gff3"/>
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
106 <output name="output" format="gff3">
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
107 <assert_contents>
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
108 <has_text text="polypeptide" />
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
109 </assert_contents>
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
110 </output>
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
111 </test>
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
112 </tests>
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
113 <help>
0
28067ed4ea0e Docker support and update for protk 1.4
iracooke
parents:
diff changeset
114
28067ed4ea0e Docker support and update for protk 1.4
iracooke
parents:
diff changeset
115 **What it does**
28067ed4ea0e Docker support and update for protk 1.4
iracooke
parents:
diff changeset
116
28067ed4ea0e Docker support and update for protk 1.4
iracooke
parents:
diff changeset
117 Exports peptides and proteins to gff
28067ed4ea0e Docker support and update for protk 1.4
iracooke
parents:
diff changeset
118
2
68d8c9e521d7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 0
diff changeset
119 </help>
0
28067ed4ea0e Docker support and update for protk 1.4
iracooke
parents:
diff changeset
120 </tool>