diff heatmap.bin.xml @ 0:b0718c06e329 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/heatmap.bin.xml	Fri May 19 04:56:10 2017 -0400
@@ -0,0 +1,137 @@
+<tool profile="16.07" id="mothur_heatmap_bin" name="Heatmap.bin" version="@WRAPPER_VERSION@.0">
+    <description>Generate a heatmap for OTUs</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <expand macro="version_command"/>
+    <command><![CDATA[
+        @SHELL_OPTIONS@
+
+        ## create symlinks to input datasets
+        ln -s "$input.otu" input_otu.dat &&
+
+        echo 'heatmap.bin(
+            #if $input.otu.is_of_type("mothur.rabund"):
+                rabund=input_otu.dat,
+            #elif $input.otu.is_of_type("mothur.sabund"):
+                sabund=input_otu.dat,
+            #elif $input.otu.is_of_type("mothur.list"):
+                list=input_otu.dat,
+            #elif $input.otu.is_of_type("mothur.relabund"):
+                relabund=input_otu.dat,
+            #elif $input.otu.is_of_type("mothur.shared"):
+                shared=input_otu.dat,
+            #end if
+            #if $input.has_groups == 'yes' and $input.groups:
+                groups=${ str($input.groups).replace(",","-") },
+            #end if
+            #if $input.label:
+                label=${ str($input.label).replace(",","-") },
+            #end if
+            scale=$scale,
+            sorted=$sorted,
+            numotu=$numotu,
+            fontsize=$fontsize
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+        | tee mothur.out.log
+    ]]></command>
+    <inputs>
+        <conditional name="input">
+            <param name="has_groups" type="select" label="Generate Heatmap for">
+                <option value="no">list, rabund, sabund</option>
+                <option value="yes">shared, relabund</option>
+            </param>
+            <when value="no">
+                <param name="otu" type="data" format="mothur.list,mothur.rabund,mothur.sabund" label="list,rabund,sabund - OTU List"/>
+                <param name="label" type="select" label="label - OTU Labels" multiple="true">
+                    <expand macro="labeloptions"/>
+                </param>
+            </when>
+            <when value="yes">
+                <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared or relabund file - OTU List"/>
+                <param name="groups" type="select" multiple="true" label="groups - Groups to include">
+                    <options>
+                        <filter type="data_meta" ref="otu" key="groups"/>
+                    </options>
+                </param>
+                <param name="label" type="select" multiple="true" label="label - OTU Labels">
+                    <expand macro="labeloptions"/>
+                </param>
+            </when>
+        </conditional>
+        <param name="scale" type="select" label="scale - Scaling for heatmap">
+            <option value="log10" selected="true">Log10</option>
+            <option value="log2">Log2</option>
+            <option value="linear">Linear</option>
+        </param>
+        <param name="sorted" type="select" label="sorted - Sort heatmap">
+            <option value="shared" selected="true">By shared</option>
+            <option value="none">Don't sort</option>
+            <option value="topotu">By Total OTUs</option>
+            <option value="topgroup">By Total Groups</option>
+        </param>
+        <param name="numotu" type="integer" value="0" min="0" label="numotu - Limit the number of OTUs displayed (ignored if 0)"/>
+        <param name="fontsize" type="integer" value="24" min="0" max="100" label="fontsize - Fontsize (default is 24)"/>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <collection name="heatmaps" type="list" label="${tool.name} on ${on_string}: Heatmaps">
+            <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.bin\.svg"/>
+        </collection>
+    </outputs>
+    <tests>
+        <test>
+            <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
+            <param name="has_groups" value="no"/>
+            <output_collection name="heatmaps" count="36">
+                <element name="0.26.heatmap" md5="8f0d5cb95808115e50729e6df60629cc"/>
+            </output_collection>
+            <expand macro="logfile-test"/>
+        </test>
+        <test>
+            <param name="otu" value="amazon.an.relabund" ftype="mothur.relabund"/>
+            <param name="has_groups" value="yes"/>
+            <param name="groups" value="forest"/>
+            <param name="label" value="0.26"/>
+            <output_collection name="heatmaps" count="1">
+                <element name="0.26.heatmap" md5="b2b46b7e55f55e2b260cd6dc6ccb4485"/>
+            </output_collection>
+            <expand macro="logfile-test"/>
+        </test>
+        <test>
+            <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
+            <param name="has_groups" value="yes"/>
+            <param name="label" value="0.03,0.26,0.55"/>
+            <param name="groups" value="forest,pasture"/>
+            <param name="fontsize" value="100"/>
+            <param name="scale" value="linear"/>
+            <param name="sorted" value="none"/>
+            <output_collection name="heatmaps" count="3">
+                <element name="0.26.heatmap" md5="b46ed47e441a30588f60e1554ff703bb"/>
+            </output_collection>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+
+**Command Documentation**
+
+The heatmap.bin_ command generates a heat map from data provided in either a list_ or a shared_ file.
+
+.. _list: https://www.mothur.org/wiki/List_file
+.. _shared: https://www.mothur.org/wiki/Shared_file
+.. _heatmap.bin: https://www.mothur.org/wiki/Heatmap.bin
+
+v.1.21.0: Updated to Mothur 1.33
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>