diff stacks_stats.xml @ 0:fe6be53294c9 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/stacks_stats.xml	Thu Apr 27 04:18:05 2017 -0400
@@ -0,0 +1,82 @@
+<tool id="stacks_stats" name="Stacks: statistics" version="@WRAPPER_VERSION@.0">
+    <description>on stacks found for multiple samples</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <command><![CDATA[
+        mkdir stacks_inputs
+
+        &&
+
+        #for $input_file in $input_col
+            #set $ext = ""
+            #if not str($input_file.element_identifier).endswith('.tsv')
+                #set $ext = ".tsv"
+            #end if
+            ln -s '${input_file}' 'stacks_inputs/${input_file.element_identifier}${ext}' &&
+        #end for
+
+        stacks_summary.py --stacks-prog '$program' --res-dir stacks_inputs --logfile '$logfile' --summary summary.html
+    ]]></command>
+
+    <inputs>
+
+        <param name="program" type="select" argument="--stacks-prog" label="Program which generated the stacks">
+            <option value="ustacks">ustacks (denovo)</option>
+            <option value="pstacks">pstacks (refmap)</option>
+        </param>
+
+        <param name="logfile" argument="--logfile" format="txt" type="data" label="Log generated by the program" />
+
+        <param name="input_col" format="tabular,txt" type="data_collection" collection_type="list" label="Output from ustacks or pstacks" />
+    </inputs>
+
+    <outputs>
+        <data format="html" name="output_summary" label="Summary from ${tool.name} on ${on_string}" from_work_dir="summary.html" />
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="program" value="ustacks"/>
+            <param name="logfile" ftype="txt" value="ustacks/ustacks.out"/>
+            <param name="input_col">
+                <collection type="list">
+                    <element name="batch_1.catalog.alleles.tsv" ftype="tabular" value="genotypes/batch_1.catalog.alleles.tsv" />
+                    <element name="batch_1.catalog.snps.tsv" ftype="tabular" value="genotypes/batch_1.catalog.snps.tsv" />
+                    <element name="batch_1.catalog.tags.tsv" ftype="tabular" value="genotypes/batch_1.catalog.tags.tsv" />
+                    <element name="PopA_01.alleles.tsv" ftype="tabular" value="genotypes/PopA_01.alleles.tsv" />
+                    <element name="PopA_01.matches.tsv" ftype="tabular" value="genotypes/PopA_01.matches.tsv" />
+                    <element name="PopA_01.snps.tsv" ftype="tabular" value="genotypes/PopA_01.snps.tsv" />
+                    <element name="PopA_01.tags.tsv" ftype="tabular" value="genotypes/PopA_01.tags.tsv" />
+                    <element name="PopA_02.alleles.tsv" ftype="tabular" value="genotypes/PopA_02.alleles.tsv" />
+                    <element name="PopA_02.matches.tsv" ftype="tabular" value="genotypes/PopA_02.matches.tsv" />
+                    <element name="PopA_02.snps.tsv" ftype="tabular" value="genotypes/PopA_02.snps.tsv" />
+                    <element name="PopA_02.tags.tsv" ftype="tabular" value="genotypes/PopA_02.tags.tsv" />
+               </collection>
+            </param>
+
+            <output name="output_summary">
+                <assert_contents>
+                    <has_text text="Stacks Statistics" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+
+    <help>
+<![CDATA[
+.. class:: infomark
+
+**What it does**
+
+When given the output of ustacks or pstacks, this will generate a report containing various statistics about the detected stacks in a set of samples.
+
+--------
+
+@STACKS_INFOS@
+]]>
+    </help>
+    <expand macro="citation" />
+</tool>