diff IDMassAccuracy.xml @ 11:65be0674bb70 draft

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

--- a/IDMassAccuracy.xml	Fri May 17 10:03:56 2019 -0400
+++ b/IDMassAccuracy.xml	Wed Sep 09 20:06:18 2020 +0000
@@ -1,127 +1,136 @@
 <?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: [Utilities]-->
-<tool id="IDMassAccuracy" name="IDMassAccuracy" version="2.3.0">
+<tool id="IDMassAccuracy" name="IDMassAccuracy" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
   <description>Calculates a distribution of the mass error from given mass spectra and IDs.</description>
   <macros>
     <token name="@EXECUTABLE@">IDMassAccuracy</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[IDMassAccuracy
+  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
+@EXT_FOO@
+#import re
 
--in
-  #for token in $param_in:
-    $token
-  #end for
--id_in
-  #for token in $param_id_in:
-    $token
-  #end for
-#if $param_precursor_out:
-  -precursor_out $param_precursor_out
+## Preprocessing
+mkdir in &&
+${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
+mkdir id_in &&
+${ ' '.join(["ln -s '%s' 'id_in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $id_in if _]) }
+#if "out_precursor_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  mkdir out_precursor &&
+#end if
+#if "out_fragment_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  mkdir out_fragment &&
+#end if
+#if "out_precursor_fit_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  mkdir out_precursor_fit &&
+#end if
+#if "out_fragment_fit_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  mkdir out_fragment_fit &&
 #end if
 
-#if $rep_param_precursor_columns:
--precursor_columns
-  #for token in $rep_param_precursor_columns:
-    #if " " in str(token):
-      "$token.param_precursor_columns"
-    #else
-      $token.param_precursor_columns
-    #end if
-  #end for
+## Main program call
+
+set -o pipefail &&
+@EXECUTABLE@ -write_ctd ./ &&
+python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
+@EXECUTABLE@ -ini @EXECUTABLE@.ctd
+-in
+${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
+-id_in
+${' '.join(["'id_in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $id_in if _])}
+#if "out_precursor_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  -out_precursor
+  'out_precursor/output.${gxy2omsext("tabular")}'
 #end if
-#if $param_precursor_error_ppm:
-  -precursor_error_ppm
+#if "out_fragment_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  -out_fragment
+  'out_fragment/output.${gxy2omsext("tabular")}'
 #end if
-#if $param_fragment_out:
-  -fragment_out $param_fragment_out
+#if "out_precursor_fit_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  -out_precursor_fit
+  'out_precursor_fit/output.${gxy2omsext("tabular")}'
+#end if
+#if "out_fragment_fit_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  -out_fragment_fit
+  'out_fragment_fit/output.${gxy2omsext("tabular")}'
+#end if
+#if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
+  | tee '$stdout'
 #end if
 
-#if $rep_param_fragment_columns:
--fragment_columns
-  #for token in $rep_param_fragment_columns:
-    #if " " in str(token):
-      "$token.param_fragment_columns"
-    #else
-      $token.param_fragment_columns
-    #end if
-  #end for
+## Postprocessing
+#if "out_precursor_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  && mv 'out_precursor/output.${gxy2omsext("tabular")}' '$out_precursor'
 #end if
-#if $param_fragment_error_ppm:
-  -fragment_error_ppm
+#if "out_fragment_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  && mv 'out_fragment/output.${gxy2omsext("tabular")}' '$out_fragment'
 #end if
-#if $param_fragment_mass_tolerance:
-  -fragment_mass_tolerance $param_fragment_mass_tolerance
+#if "out_precursor_fit_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  && mv 'out_precursor_fit/output.${gxy2omsext("tabular")}' '$out_precursor_fit'
 #end if
-#if $param_separator:
-  -separator     "$param_separator"
-#end if
-#if $adv_opts.adv_opts_selector=='advanced':
-    #if $adv_opts.param_number_of_bins:
-  -number_of_bins $adv_opts.param_number_of_bins
+#if "out_fragment_fit_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  && mv 'out_fragment_fit/output.${gxy2omsext("tabular")}' '$out_fragment_fit'
 #end if
-    #if $adv_opts.param_generate_gnuplot_scripts:
-  -generate_gnuplot_scripts
-#end if
-    #if $adv_opts.param_force:
-  -force
-#end if
-#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="mzml" multiple="true" optional="False" size="30" label="Input mzML file list, containing the spectra" help="(-in) ">
-      <sanitizer>
-        <valid initial="string.printable">
-          <remove value="'"/>
-          <remove value="&quot;"/>
-        </valid>
-      </sanitizer>
-    </param>
-    <param name="param_id_in" type="data" format="idxml" multiple="true" optional="False" size="30" label="Input idXML file list, containing the identifications" help="(-id_in) ">
-      <sanitizer>
-        <valid initial="string.printable">
-          <remove value="'"/>
-          <remove value="&quot;"/>
-        </valid>
-      </sanitizer>
-    </param>
-    <repeat name="rep_param_precursor_columns" min="0" max="1" title="param_precursor_columns">
-      <param name="param_precursor_columns" display="radio" type="select" optional="True" value="MassDifference" label="Columns which will be written to the output file" help="(-precursor_columns) ">
-        <option value="MassDifference">MassDifference</option>
+    <param name="in" argument="-in" type="data" format="mzml" multiple="true" optional="false" label="Input mzML file list, containing the spectra" help=" select mzml data sets(s)"/>
+    <param name="id_in" argument="-id_in" type="data" format="idxml" multiple="true" optional="false" label="Input idXML file list, containing the identifications" help=" select idxml data sets(s)"/>
+    <param name="precursor_error_ppm" argument="-precursor_error_ppm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If this flag is used, the precursor mass tolerances are estimated in ppm instead of Da" help=""/>
+    <param name="fragment_error_ppm" argument="-fragment_error_ppm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If this flag is used, the fragment mass tolerances are estimated in ppm instead of Da" help=""/>
+    <param name="fragment_mass_tolerance" argument="-fragment_mass_tolerance" type="float" optional="true" value="0.5" label="Maximal fragment mass tolerance which is allowed for MS/MS spectra, used for the calculation of matching ions" help=""/>
+    <expand macro="adv_opts_macro">
+      <param name="number_of_bins" argument="-number_of_bins" type="integer" optional="true" min="10" value="100" label="Number of bins that should be used to calculate the histograms for the fitting" help=""/>
+      <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>
-    </repeat>
-    <param name="param_precursor_error_ppm" display="radio" type="boolean" truevalue="-precursor_error_ppm" falsevalue="" checked="false" optional="True" label="If this flag is used, the precursor mass tolerances are estimated in ppm instead of Da" help="(-precursor_error_ppm) "/>
-    <repeat name="rep_param_fragment_columns" min="0" max="1" title="param_fragment_columns">
-      <param name="param_fragment_columns" display="radio" type="select" optional="True" value="MassDifference" label="Columns which will be written to the output file" help="(-fragment_columns) ">
-        <option value="MassDifference">MassDifference</option>
-      </param>
-    </repeat>
-    <param name="param_fragment_error_ppm" display="radio" type="boolean" truevalue="-fragment_error_ppm" falsevalue="" checked="false" optional="True" label="If this flag is used, the fragment mass tolerances are estimated in ppm instead of Da" help="(-fragment_error_ppm) "/>
-    <param name="param_fragment_mass_tolerance" type="float" value="0.5" label="Maximal fragment mass tolerance which is allowed for MS/MS spectra, used for the calculation of matching ions" help="(-fragment_mass_tolerance) "/>
-    <param name="param_separator" type="text" size="30" value=" " label="character which should be used to separate the columns in the output files" help="(-separator) ">
-      <sanitizer>
-        <valid initial="string.printable">
-          <remove value="'"/>
-          <remove value="&quot;"/>
-        </valid>
-      </sanitizer>
+    </expand>
+    <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="false">
+      <option value="out_precursor_FLAG">out_precursor (Enables the test mode (needed for internal use only))</option>
+      <option value="out_fragment_FLAG">out_fragment (Enables the test mode (needed for internal use only))</option>
+      <option value="out_precursor_fit_FLAG">out_precursor_fit (Enables the test mode (needed for internal use only))</option>
+      <option value="out_fragment_fit_FLAG">out_fragment_fit (Enables the test mode (needed for internal use only))</option>
+      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
     </param>
-    <expand macro="advanced_options">
-      <param name="param_number_of_bins" type="integer" min="10" optional="True" value="100" label="Number of bins that should be used to calculate the histograms for the fitting" help="(-number_of_bins) "/>
-      <param name="param_generate_gnuplot_scripts" display="radio" type="boolean" truevalue="-generate_gnuplot_scripts" falsevalue="" checked="false" optional="True" label="If this option is set to true, the distributions and the fits are used to generate a gnuplot script, that can be used to generate plots" help="(-generate_gnuplot_scripts) The options 'precursor_out' and 'fragment_out' must be set to take this effect"/>
-      <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
-    </expand>
   </inputs>
   <outputs>
-    <data name="param_precursor_out" format="tabular"/>
-    <data name="param_fragment_out" format="tabular"/>
+    <data name="out_precursor" label="${tool.name} on ${on_string}: out_precursor" format="tabular">
+      <filter>OPTIONAL_OUTPUTS is not None and "out_precursor_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
+    <data name="out_fragment" label="${tool.name} on ${on_string}: out_fragment" format="tabular">
+      <filter>OPTIONAL_OUTPUTS is not None and "out_fragment_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
+    <data name="out_precursor_fit" label="${tool.name} on ${on_string}: out_precursor_fit" format="tabular">
+      <filter>OPTIONAL_OUTPUTS is not None and "out_precursor_fit_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
+    <data name="out_fragment_fit" label="${tool.name} on ${on_string}: out_fragment_fit" format="tabular">
+      <filter>OPTIONAL_OUTPUTS is not None and "out_fragment_fit_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
+    <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
+      <filter>OPTIONAL_OUTPUTS is None</filter>
+    </data>
+    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
+      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
   </outputs>
-  <help>Calculates a distribution of the mass error from given mass spectra and IDs.
+  <tests>
+    <expand macro="autotest_IDMassAccuracy"/>
+    <expand macro="manutest_IDMassAccuracy"/>
+  </tests>
+  <help><![CDATA[Calculates a distribution of the mass error from given mass spectra and IDs.
 
 
-For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_IDMassAccuracy.html</help>
+For more information, visit http://www.openms.de/documentation/UTILS_IDMassAccuracy.html]]></help>
+  <expand macro="references"/>
 </tool>