diff columnArrange.xml @ 0:f18f67056946 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header commit 088e73e958b55dc765778641b8a84080cc289f85-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/columnArrange.xml	Fri Oct 16 14:31:13 2015 -0400
@@ -0,0 +1,83 @@
+<tool id="bg_column_arrange_by_header" name="Column arrange" version="0.1">
+    <description>by header name</description>
+    <requirements>
+        <requirement type="package" version="0.14.1">pandas</requirement>
+    </requirements>
+    <command interpreter="python">
+    <![CDATA[
+        column_arrange.py
+          --columns
+        #for token in $rep_param_columns:
+            "$token.param_column"
+        #end for
+        --in $param_input
+        --out $output
+    ]]>
+    </command>
+    <inputs>
+        <param format="tabular" name="param_input" type="data" label="file to rearrange" />
+        <repeat name ="rep_param_columns" min="1" title="Specify the first few columns by name">
+            <param name="param_column" type="text" value="" label="column">
+                <sanitizer>
+                    <valid initial="string.printable">
+                        <remove value="&apos;"/>
+                    </valid>
+                </sanitizer>
+            </param>
+        </repeat>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="output" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="param_input" value="columnarrange_input1.tab"/>
+            <repeat name="rep_param_columns">
+                <param name="param_column" value="fname"/>
+            </repeat>
+            <repeat name="rep_param_columns">
+                <param name="param_column" value="age"/>
+            </repeat>
+            <output name="out" file="columnarrange_result1.tab"/>
+        </test>
+        <test>
+            <param name="param_input" value="columnarrange_input2.tab"/>
+            <repeat name="rep_param_columns">
+                <param name="param_column" value="first name"/>
+            </repeat>
+            <repeat name="rep_param_columns">
+                <param name="param_column" value="nationality"/>
+            </repeat>
+            <output name="out" file="columnarrange_result2.tab"/>
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+With this tool you can specify (by naming the header) which columns need to be leftmost.
+The columns which are not specified will be ordered as before, right of the columns which were specified.
+
+Input file::
+
+    AHeader BHeader CHeader DHeader
+    a       b       c       d
+    a       b       c       d
+
+Specifying **CHeader** and **BHeader**, as the columns that should be leftmost, generates::
+
+    CHeader BHeader AHeader DHeader
+    c       b       a       d
+    c       b       a       d
+
+    </help>
+    <citations>
+        <citation type="bibtex">
+            @ARTICLE{bgruening_galaxytools,
+                Author = {Björn Grüning, Cameron Smith, Torsten Houwaart, Nicola Soranzo, Eric Rasche},
+                keywords = {bioinformatics, ngs, galaxy, cheminformatics, rna},
+                title = {{Galaxy Tools - A collection of bioinformatics and cheminformatics tools for the Galaxy environment}},
+                url = {https://github.com/bgruening/galaxytools}
+            }
+        </citation>
+    </citations>
+</tool>