Mercurial > repos > galaxyp > openms_openswathrewritetofeaturexml
comparison OpenSwathRewriteToFeatureXML.xml @ 7:63e463c4abc1 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
author | galaxyp |
---|---|
date | Wed, 15 May 2019 08:25:01 -0400 |
parents | 27dc92c6a49b |
children | 175016416031 |
comparison
equal
deleted
inserted
replaced
6:99d514749a9c | 7:63e463c4abc1 |
---|---|
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>OpenSwathRewriteToFeatureXML | 13 <command detect_errors="aggressive"><![CDATA[OpenSwathRewriteToFeatureXML |
14 | 14 |
15 #if $param_csv: | 15 #if $param_csv: |
16 -csv $param_csv | 16 -csv $param_csv |
17 #end if | 17 #end if |
18 #if $param_featureXML: | 18 #if $param_featureXML: |
27 #if $adv_opts.adv_opts_selector=='advanced': | 27 #if $adv_opts.adv_opts_selector=='advanced': |
28 #if $adv_opts.param_force: | 28 #if $adv_opts.param_force: |
29 -force | 29 -force |
30 #end if | 30 #end if |
31 #end if | 31 #end if |
32 </command> | 32 ]]></command> |
33 <inputs> | 33 <inputs> |
34 <param name="param_csv" type="data" format="tabular" optional="True" label="mProphet tsv output file: "all_peakgroups.xls"" help="(-csv) "/> | 34 <param name="param_csv" type="data" format="tabular" optional="True" label="mProphet tsv output file: "all_peakgroups.xls"" help="(-csv) "/> |
35 <param name="param_featureXML" type="data" format="featurexml" optional="False" label="input featureXML file" help="(-featureXML) "/> | 35 <param name="param_featureXML" type="data" format="featurexml" optional="False" label="input featureXML file" help="(-featureXML) "/> |
36 <param name="param_FDR_cutoff" type="float" value="-1.0" label="FDR cutoff (" help="(-FDR_cutoff) e.g. to remove all features with a an m_score above 0.05 use 0.05 here)"/> | 36 <param name="param_FDR_cutoff" type="float" value="-1.0" label="FDR cutoff (" help="(-FDR_cutoff) e.g. to remove all features with a an m_score above 0.05 use 0.05 here)"/> |
37 <expand macro="advanced_options"> | 37 <expand macro="advanced_options"> |
42 <data name="param_out" format="featurexml"/> | 42 <data name="param_out" format="featurexml"/> |
43 </outputs> | 43 </outputs> |
44 <help>Combines featureXML and mProphet tsv to FDR filtered featureXML. | 44 <help>Combines featureXML and mProphet tsv to FDR filtered featureXML. |
45 | 45 |
46 | 46 |
47 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_OpenSwathRewriteToFeatureXML.html</help> | 47 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_OpenSwathRewriteToFeatureXML.html</help> |
48 </tool> | 48 </tool> |