Mercurial > repos > galaxyp > openms_idfileconverter

comparison IDFileConverter.xml @ 2:5588e443a7db draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 50c26f7fbe8a2bd1347c860d7a62480865efc254
author galaxyp
date Thu, 27 Apr 2017 13:23:15 -0400
parents f700da3ba35f
children 066cf4d993f5
comparison
equal deleted inserted replaced
1:f700da3ba35f 2:5588e443a7db
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 </macros> 9 </macros>
10 <expand macro="references"/> 10 <expand macro="references"/>
11 <expand macro="stdio"/> 11 <expand macro="stdio"/>
12 <expand macro="requirements"/> 12 <expand macro="requirements"/>
13 <command>IDFileConverter 13 <command><![CDATA[
14
15 ## check input file type
16 #set $in_type = $param_in.ext
14 17
15 #if $param_in: 18 ## create the symlinks to set the proper file extension, since IDFileConverter uses them to choose how to handle the input files
16 -in $param_in 19 ln -s '$param_in' 'param_in.${in_type}' &&
17 #end if 20
18 #if $param_out: 21 IDFileConverter
19 -out $param_out 22
20 #end if 23 #if $param_in:
21 #if $param_out_type: 24 -in 'param_in.${in_type}'
22 -out_type
23 #if " " in str($param_out_type):
24 "$param_out_type"
25 #else
26 $param_out_type
27 #end if 25 #end if
28 #end if 26 #if $param_out:
29 #if $param_mz_file: 27 -out $param_out
30 -mz_file $param_mz_file
31 #end if
32 #if $param_mz_name:
33 -mz_name "$param_mz_name"
34 #end if
35 #if $param_peptideprophet_analyzed:
36 -peptideprophet_analyzed
37 #end if
38 #if $param_score_type:
39 -score_type
40 #if " " in str($param_score_type):
41 "$param_score_type"
42 #else
43 $param_score_type
44 #end if 28 #end if
45 #end if 29 #if $param_out_type:
46 #if $adv_opts.adv_opts_selector=='advanced': 30 -out_type
47 #if $adv_opts.param_ignore_proteins_per_peptide: 31 #if " " in str($param_out_type):
48 -ignore_proteins_per_peptide 32 "$param_out_type"
49 #end if 33 #else
50 #if $adv_opts.param_scan_regex: 34 $param_out_type
51 -scan_regex "$adv_opts.param_scan_regex" 35 #end if
52 #end if 36 #end if
53 #if $adv_opts.param_force: 37 #if $param_mz_file:
54 -force 38 -mz_file $param_mz_file
55 #end if 39 #end if
56 #end if 40 #if $param_mz_name:
41 -mz_name "$param_mz_name"
42 #end if
43 #if $param_peptideprophet_analyzed:
44 -peptideprophet_analyzed
45 #end if
46 #if $param_score_type:
47 -score_type
48 #if " " in str($param_score_type):
49 "$param_score_type"
50 #else
51 $param_score_type
52 #end if
53 #end if
54 #if $adv_opts.adv_opts_selector=='advanced':
55 #if $adv_opts.param_ignore_proteins_per_peptide:
56 -ignore_proteins_per_peptide
57 #end if
58 #if $adv_opts.param_scan_regex:
59 -scan_regex "$adv_opts.param_scan_regex"
60 #end if
61 #if $adv_opts.param_force:
62 -force
63 #end if
64 #end if
65 ]]>
57 </command> 66 </command>
58 <inputs> 67 <inputs>
59 <param name="param_in" type="data" format="tabular,mzid,pepxml,idxml" optional="False" label="Input file or directory containing the data to convert" help="(-in) This may be: &lt;br&gt;- a single file in a multi-purpose XML format (pepXML, protXML, idXML, mzid), &lt;br&gt;- a single file in a search engine-specific format (Mascot: mascotXML, OMSSA: omssaXML, X! Tandem: xml, Percolator: psms), &lt;br&gt;- a single text file (tab separated) with one line for all peptide sequences matching a spectrum (top N hits), &lt;br&gt;- for Sequest results, a directory containing .out files. &lt;br&gt;"/> 68 <param name="param_in" type="data" format="tabular,mzid,pepxml,idxml" optional="False" label="Input file or directory containing the data to convert" help="(-in) This may be: &lt;br&gt;- a single file in a multi-purpose XML format (pepXML, protXML, idXML, mzid), &lt;br&gt;- a single file in a search engine-specific format (Mascot: mascotXML, OMSSA: omssaXML, X! Tandem: xml, Percolator: psms), &lt;br&gt;- a single text file (tab separated) with one line for all peptide sequences matching a spectrum (top N hits), &lt;br&gt;- for Sequest results, a directory containing .out files. &lt;br&gt;"/>
60 <param name="param_out_type" display="radio" type="select" optional="True" label="Output file type (default: determined from file extension)" help="(-out_type) "> 69 <param name="param_out_type" display="radio" type="select" optional="True" label="Output file type (default: determined from file extension)" help="(-out_type) ">
61 <option value="idXML">idXML</option> 70 <option value="idXML">idXML</option>
90 </param> 99 </param>
91 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 100 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
92 </expand> 101 </expand>
93 </inputs> 102 </inputs>
94 <outputs> 103 <outputs>
95 <data name="param_out" format="mzid"/> 104 <data name="param_out" auto_format="true"/>
96 </outputs> 105 </outputs>
97 <help>Converts identification engine file formats. 106 <help>Converts identification engine file formats.
98 107
99 108
100 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDFileConverter.html</help> 109 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDFileConverter.html</help>