Mercurial > repos > galaxyp > openms_idfileconverter
comparison IDFileConverter.xml @ 2:5588e443a7db draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 50c26f7fbe8a2bd1347c860d7a62480865efc254
author | galaxyp |
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date | Thu, 27 Apr 2017 13:23:15 -0400 |
parents | f700da3ba35f |
children | 066cf4d993f5 |
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1:f700da3ba35f | 2:5588e443a7db |
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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: <br>- a single file in a multi-purpose XML format (pepXML, protXML, idXML, mzid), <br>- a single file in a search engine-specific format (Mascot: mascotXML, OMSSA: omssaXML, X! Tandem: xml, Percolator: psms), <br>- a single text file (tab separated) with one line for all peptide sequences matching a spectrum (top N hits), <br>- for Sequest results, a directory containing .out files. <br>"/> | 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: <br>- a single file in a multi-purpose XML format (pepXML, protXML, idXML, mzid), <br>- a single file in a search engine-specific format (Mascot: mascotXML, OMSSA: omssaXML, X! Tandem: xml, Percolator: psms), <br>- a single text file (tab separated) with one line for all peptide sequences matching a spectrum (top N hits), <br>- for Sequest results, a directory containing .out files. <br>"/> |
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> |