diff QCEmbedder.xml @ 9:254e748f243a draft

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

--- a/QCEmbedder.xml	Fri May 17 09:39:22 2019 -0400
+++ b/QCEmbedder.xml	Wed Sep 09 12:47:21 2020 +0000
@@ -1,85 +1,110 @@
 <?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="QCEmbedder" name="QCEmbedder" version="2.3.0">
+<tool id="QCEmbedder" name="QCEmbedder" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
   <description>Attaches a table or an image to a given qc parameter.</description>
   <macros>
     <token name="@EXECUTABLE@">QCEmbedder</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[QCEmbedder
+  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
+@EXT_FOO@
+#import re
 
-#if $param_in:
-  -in $param_in
+## Preprocessing
+#if $in:
+  mkdir in &&
+  ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 #end if
-#if $param_qp_att_acc:
-  -qp_att_acc     "$param_qp_att_acc"
-#end if
-#if $param_cv_acc:
-  -cv_acc     "$param_cv_acc"
+#if $run:
+  mkdir run &&
+  ln -s '$run' 'run/${re.sub("[^\w\-_]", "_", $run.element_identifier)}.$gxy2omsext($run.ext)' &&
 #end if
-#if $param_run:
-  -run $param_run
+#if $plot:
+  mkdir plot &&
+  ln -s '$plot' 'plot/${re.sub("[^\w\-_]", "_", $plot.element_identifier)}.$gxy2omsext($plot.ext)' &&
 #end if
-#if $param_name:
-  -name     "$param_name"
-#end if
-#if $param_plot:
-  -plot $param_plot
+#if $table:
+  mkdir table &&
+  ln -s '$table' 'table/${re.sub("[^\w\-_]", "_", $table.element_identifier)}.$gxy2omsext($table.ext)' &&
 #end if
-#if $param_table:
-  -table $param_table
+mkdir out &&
+
+## Main program call
+
+set -o pipefail &&
+@EXECUTABLE@ -write_ctd ./ &&
+python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
+@EXECUTABLE@ -ini @EXECUTABLE@.ctd
+#if $in:
+  -in
+  'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
 #end if
-#if $param_out:
-  -out $param_out
-#end if
-#if $adv_opts.adv_opts_selector=='advanced':
-    #if $adv_opts.param_force:
-  -force
+#if $run:
+  -run
+  'run/${re.sub("[^\w\-_]", "_", $run.element_identifier)}.$gxy2omsext($run.ext)'
 #end if
+#if $plot:
+  -plot
+  'plot/${re.sub("[^\w\-_]", "_", $plot.element_identifier)}.$gxy2omsext($plot.ext)'
 #end if
-]]></command>
+#if $table:
+  -table
+  'table/${re.sub("[^\w\-_]", "_", $table.element_identifier)}.$gxy2omsext($table.ext)'
+#end if
+-out
+'out/output.${gxy2omsext("qcml")}'
+
+## Postprocessing
+&& mv 'out/output.${gxy2omsext("qcml")}' '$out'
+#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="qcml" optional="True" label="Input qcml file" help="(-in) "/>
-    <param name="param_qp_att_acc" type="text" size="30" label="Defines the qp cv accession of the qp to which the table/image is attached" help="(-qp_att_acc) ">
-      <sanitizer>
-        <valid initial="string.printable">
-          <remove value="'"/>
-          <remove value="&quot;"/>
-        </valid>
-      </sanitizer>
+    <param name="in" argument="-in" type="data" format="qcml" optional="true" label="Input qcml file" help=" select qcml data sets(s)"/>
+    <param name="qp_att_acc" argument="-qp_att_acc" type="text" optional="true" value="" label="Defines the qp cv accession of the qp to which the table/image is attached" help="">
+      <expand macro="list_string_san"/>
     </param>
-    <param name="param_cv_acc" type="text" size="30" label="Defines the cv accession of the attachment" help="(-cv_acc) ">
-      <sanitizer>
-        <valid initial="string.printable">
-          <remove value="'"/>
-          <remove value="&quot;"/>
-        </valid>
-      </sanitizer>
+    <param name="cv_acc" argument="-cv_acc" type="text" optional="false" value="" label="Defines the cv accession of the attachment" help="">
+      <expand macro="list_string_san"/>
+    </param>
+    <param name="run" argument="-run" type="data" format="mzml" optional="true" label="The file that defined the run under which the qp for the attachment is aggregated as mzML file" help="The file is only used to extract the run name from the file name select mzml data sets(s)"/>
+    <param name="name" argument="-name" type="text" optional="true" value="" label="If no file for the run was given (or if the target qp is contained in a set), at least a name of the target run/set containing the the qp for the attachment has to be given" help="">
+      <expand macro="list_string_san"/>
     </param>
-    <param name="param_run" type="data" format="mzml" optional="True" label="The file that defined the run under which the qp for the attachment is aggregated as mzML file" help="(-run) The file is only used to extract the run name from the file name"/>
-    <param name="param_name" type="text" size="30" label="If no file for the run was given (or if the target qp is contained in a set), at least a name of the target run/set containing the the qp for the attachment has to be given" help="(-name) ">
-      <sanitizer>
-        <valid initial="string.printable">
-          <remove value="'"/>
-          <remove value="&quot;"/>
-        </valid>
-      </sanitizer>
+    <param name="plot" argument="-plot" type="data" format="png" optional="true" label="If a plot image is to be attached to a qp, this has to be specified here" help=" select png data sets(s)"/>
+    <param name="table" argument="-table" type="data" format="csv" optional="true" label="If a table is to be attached to a qp, this has to be specified here" help=" select csv data sets(s)"/>
+    <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="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
     </param>
-    <param name="param_plot" type="data" format="PNG" optional="True" label="If a plot image is to be attached to a qp, this has to be specified here" help="(-plot) "/>
-    <param name="param_table" type="data" format="tabular" optional="True" label="If a table is to be attached to a qp, this has to be specified here" help="(-table) "/>
-    <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) "/>
-    </expand>
   </inputs>
   <outputs>
-    <data name="param_out" format="qcml"/>
+    <data name="out" label="${tool.name} on ${on_string}: out" format="qcml"/>
+    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
+      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
   </outputs>
-  <help>Attaches a table or an image to a given qc parameter.
+  <tests>
+    <expand macro="autotest_QCEmbedder"/>
+    <expand macro="manutest_QCEmbedder"/>
+  </tests>
+  <help><![CDATA[Attaches a table or an image to a given qc parameter.
 
 
-For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_QCEmbedder.html</help>
+For more information, visit http://www.openms.de/documentation/UTILS_QCEmbedder.html]]></help>
+  <expand macro="references"/>
 </tool>