diff QCShrinker.xml @ 0:2092c98a7c43 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/QCShrinker.xml	Wed Mar 01 12:54:11 2017 -0500
@@ -0,0 +1,76 @@
+<?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 CTD2Galaxy.-->
+<!--Proposed Tool Section: [Utilities]-->
+<tool id="QCShrinker" name="QCShrinker" version="2.1.0">
+  <description>This application is used to remove the verbose table attachments from a qcml file that are not needed anymore, e.g. for a final report.</description>
+  <macros>
+    <token name="@EXECUTABLE@">QCShrinker</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="references"/>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>QCShrinker
+
+#if $param_in:
+  -in $param_in
+#end if
+
+#if $rep_param_qp_accessions:
+-qp_accessions
+  #for token in $rep_param_qp_accessions:
+    #if " " in str(token):
+      "$token.param_qp_accessions"
+    #else
+      $token.param_qp_accessions
+    #end if
+  #end for
+#end if
+#if $param_name:
+  -name     "$param_name"
+#end if
+#if $param_run:
+  -run $param_run
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_force:
+  -force
+#end if
+#end if
+</command>
+  <inputs>
+    <param name="param_in" type="data" format="qcml" optional="False" label="Input qcml file" help="(-in) "/>
+    <repeat name="rep_param_qp_accessions" min="0" max="1" title="param_qp_accessions">
+      <param name="param_qp_accessions" type="text" size="30" label="A list of cv accessions that should be removed" help="(-qp_accessions) If empty, the usual suspects will be removed!">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+    </repeat>
+    <param name="param_name" type="text" size="30" label="The name of the target run or set that contains the requested quality paramete" help="(-name) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_run" type="data" format="mzml" optional="True" label="The file from which the name of the target run that contains the requested quality parameter is taken" help="(-run) This overrides the name parameter!"/>
+    <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"/>
+  </outputs>
+  <help>This application is used to remove the verbose table attachments from a qcml file that are not needed anymore, e.g. for a final report.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_QCShrinker.html</help>
+</tool>