diff QCEmbedder.xml @ 0:66aa3156aeb5 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/QCEmbedder.xml	Wed Mar 01 12:52:50 2017 -0500
@@ -0,0 +1,85 @@
+<?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="QCEmbedder" name="QCEmbedder" version="2.1.0">
+  <description>Attaches a table or an image to a given qc parameter.</description>
+  <macros>
+    <token name="@EXECUTABLE@">QCEmbedder</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="references"/>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>QCEmbedder
+
+#if $param_in:
+  -in $param_in
+#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"
+#end if
+#if $param_run:
+  -run $param_run
+#end if
+#if $param_name:
+  -name     "$param_name"
+#end if
+#if $param_plot:
+  -plot $param_plot
+#end if
+#if $param_table:
+  -table $param_table
+#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="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>
+    <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>
+    <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>
+    <param name="param_plot" type="data" format="" 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"/>
+  </outputs>
+  <help>Attaches a table or an image to a given qc parameter.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_QCEmbedder.html</help>
+</tool>