diff FileInfo.xml @ 11:98f171dab07c draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"

--- a/FileInfo.xml	Fri May 17 10:12:39 2019 -0400
+++ b/FileInfo.xml	Wed Sep 09 12:52:57 2020 +0000
@@ -1,72 +1,94 @@
 <?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
 <!--Proposed Tool Section: [File Handling]-->
-<tool id="FileInfo" name="FileInfo" version="2.3.0">
+<tool id="FileInfo" name="FileInfo" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
   <description>Shows basic information about the file, such as data ranges and file type.</description>
   <macros>
     <token name="@EXECUTABLE@">FileInfo</token>
     <import>macros.xml</import>
+    <import>macros_autotest.xml</import>
+    <import>macros_test.xml</import>
   </macros>
-  <expand macro="references"/>
+  <expand macro="requirements"/>
   <expand macro="stdio"/>
-  <expand macro="requirements"/>
-  <command detect_errors="aggressive"><![CDATA[FileInfo
+  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
+@EXT_FOO@
+#import re
 
-#if $param_in:
-  -in $param_in
-#end if
-#if $param_out:
-  -out $param_out
+## Preprocessing
+mkdir in &&
+ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+mkdir out &&
+#if "out_tsv_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  mkdir out_tsv &&
 #end if
-#if $param_out_tsv:
-  -out_tsv $param_out_tsv
-#end if
-#if $param_m:
-  -m
-#end if
-#if $param_p:
-  -p
-#end if
-#if $param_s:
-  -s
-#end if
-#if $param_d:
-  -d
+
+## Main program call
+
+set -o pipefail &&
+@EXECUTABLE@ -write_ctd ./ &&
+python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
+@EXECUTABLE@ -ini @EXECUTABLE@.ctd
+-in
+'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
+-out
+'out/output.${gxy2omsext("txt")}'
+#if "out_tsv_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  -out_tsv
+  'out_tsv/output.${gxy2omsext("csv")}'
 #end if
-#if $param_c:
-  -c
-#end if
-#if $param_v:
-  -v
+#if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
+  | tee '$stdout'
 #end if
-#if $param_i:
-  -i
-#end if
-#if $adv_opts.adv_opts_selector=='advanced':
-    #if $adv_opts.param_force:
-  -force
-#end if
+
+## Postprocessing
+&& mv 'out/output.${gxy2omsext("txt")}' '$out'
+#if "out_tsv_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  && mv 'out_tsv/output.${gxy2omsext("csv")}' '$out_tsv'
 #end if
-]]></command>
+#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
+  && mv '@EXECUTABLE@.ctd' '$ctd_out'
+#end if]]></command>
+  <configfiles>
+    <inputs name="args_json" data_style="paths"/>
+    <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
+  </configfiles>
   <inputs>
-    <param name="param_in" type="data" format="mzData,mzxml,mzml,dta,dta2d,mgf,featurexml,consensusxml,idxml,pepxml,fid,mzid,trafoxml,fasta" optional="False" label="input file" help="(-in) "/>
-    <param name="param_m" display="radio" type="boolean" truevalue="-m" falsevalue="" checked="false" optional="True" label="Show meta information about the whole experiment" help="(-m) "/>
-    <param name="param_p" display="radio" type="boolean" truevalue="-p" falsevalue="" checked="false" optional="True" label="Shows data processing information" help="(-p) "/>
-    <param name="param_s" display="radio" type="boolean" truevalue="-s" falsevalue="" checked="false" optional="True" label="Computes a five-number statistics of intensities, qualities, and widths" help="(-s) "/>
-    <param name="param_d" display="radio" type="boolean" truevalue="-d" falsevalue="" checked="false" optional="True" label="Show detailed listing of all spectra and chromatograms (peak files only)" help="(-d) "/>
-    <param name="param_c" display="radio" type="boolean" truevalue="-c" falsevalue="" checked="false" optional="True" label="Check for corrupt data in the file (peak files only)" help="(-c) "/>
-    <param name="param_v" display="radio" type="boolean" truevalue="-v" falsevalue="" checked="false" optional="True" label="Validate the file only (for mzML, mzData, mzXML, featureXML, idXML, consensusXML, pepXML)" help="(-v) "/>
-    <param name="param_i" display="radio" type="boolean" truevalue="-i" falsevalue="" checked="false" optional="True" label="Check whether a given mzML file contains valid indices (conforming to the indexedmzML standard)" help="(-i) "/>
-    <expand macro="advanced_options">
-      <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
+    <param name="in" argument="-in" type="data" format="consensusxml,dta,dta2d,fasta,featurexml,idxml,mgf,mzdata,mzid,mzml,mzxml,pepxml,trafoxml" optional="false" label="input file" help=" select consensusxml,dta,dta2d,fasta,featurexml,idxml,mgf,mzdata,mzid,mzml,mzxml,pepxml,trafoxml data sets(s)"/>
+    <param name="m" argument="-m" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show meta information about the whole experiment" help=""/>
+    <param name="p" argument="-p" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Shows data processing information" help=""/>
+    <param name="s" argument="-s" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Computes a five-number statistics of intensities, qualities, and widths" help=""/>
+    <param name="d" argument="-d" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show detailed listing of all spectra and chromatograms (peak files only)" help=""/>
+    <param name="c" argument="-c" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Check for corrupt data in the file (peak files only)" help=""/>
+    <param name="v" argument="-v" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Validate the file only (for mzML, mzData, mzXML, featureXML, idXML, consensusXML, pepXML)" help=""/>
+    <param name="i" argument="-i" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Check whether a given mzML file contains valid indices (conforming to the indexedmzML standard)" help=""/>
+    <expand macro="adv_opts_macro">
+      <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
+      <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+        <expand macro="list_string_san"/>
+      </param>
     </expand>
+    <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
+      <option value="out_tsv_FLAG">out_tsv (Enables the test mode (needed for internal use only))</option>
+      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
+    </param>
   </inputs>
   <outputs>
-    <data name="param_out" format="txt"/>
-    <data name="param_out_tsv" format="tabular"/>
+    <data name="out" label="${tool.name} on ${on_string}: out" format="txt"/>
+    <data name="out_tsv" label="${tool.name} on ${on_string}: out_tsv" format="csv">
+      <filter>OPTIONAL_OUTPUTS is not None and "out_tsv_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
+    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
+      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
   </outputs>
-  <help>Shows basic information about the file, such as data ranges and file type.
+  <tests>
+    <expand macro="autotest_FileInfo"/>
+    <expand macro="manutest_FileInfo"/>
+  </tests>
+  <help><![CDATA[Shows basic information about the file, such as data ranges and file type.
 
 
-For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_FileInfo.html</help>
+For more information, visit http://www.openms.de/documentation/TOPP_FileInfo.html]]></help>
+  <expand macro="references"/>
 </tool>