diff dma-filelist-generation.xml @ 0:6a2bb42acfe4 draft

planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dma-filelist-generation.xml	Tue Mar 27 06:53:36 2018 -0400
@@ -0,0 +1,63 @@
+<tool id="dma_filelist_generation" name="dma_filelist_generation" version="0.1.0">
+    <description>Generate filelist for DMA DIMS nearline</description>
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
+    <command interpreter="python"><![CDATA[
+        dma-filelist-generation.py
+        -i
+        #for $i  in  $library
+            $__app__.config.user_library_import_dir/$__user_email__/$i.library
+        #end for
+        -o .
+        #if $check_mzml
+            --check_mzml
+        #end if
+        #if $check_raw
+            --check_raw
+        #end if
+        #if $create_filelist_mzml
+            --create_filelist_mzml
+        #end if
+        #if $create_filelist_raw
+            --create_filelist_raw
+        #end if
+
+    ]]></command>
+
+    <inputs>
+
+        <repeat name="library" title="Library directories containing *.mzml or *.raw files"
+                    help="multiple directories can be used to make one filelist, for cases where
+                           the files for different classes are in different directories">
+            <param name="library" type="text" size="40" >
+                    <validator type="empty_field" />
+            </param>
+        </repeat>
+
+        <param name="check_mzml" checked="true" type="boolean" label="Check mzML files?" help=""/>
+        <param name="check_raw" checked="true" type="boolean" label="Check raw files?" help=""/>
+        <param name="create_filelist_mzml" type="boolean" label="Create filelist for mzML files?" help=""/>
+        <param name="create_filelist_raw" checked="true" type="boolean" label="Create filelist for raw files?" help=""/>
+
+
+    </inputs>
+    <outputs>
+        <data name="filelist_mzml" label="${tool.name} on ${on_string}: filelist mzML"
+              from_work_dir="filelist_mzml.tsv" format="tsv">
+            <filter>create_filelist_mzml is True</filter>
+        </data>
+        <data name="filelist_raw" label="${tool.name} on ${on_string}: filelist raw"
+              from_work_dir="filelist_raw.tsv" format="tsv">
+            <filter>create_filelist_raw is True</filter>
+        </data>
+
+    </outputs>
+    <tests>
+
+    </tests>
+    <help><![CDATA[
+
+
+    ]]></help>
+</tool>