diff biom.info.xml @ 0:c664838f087c draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/biom.info.xml	Tue Mar 20 21:53:45 2018 -0400
@@ -0,0 +1,123 @@
+<tool profile="16.07" id="mothur_biom_info" name="Biom.info" version="@WRAPPER_VERSION@.0">
+    <description>create shared and taxonomy files from biom</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <expand macro="version_command"/>
+    <command><![CDATA[
+@SHELL_OPTIONS@
+
+ln -s '$biom' input.biom &&
+
+echo 'biom.info(
+    biom=input.biom,
+    #if str($label) != '':
+        label=$label,
+    #end if
+    basis=$basis,
+    output=$output,
+    relabund=$relabund,
+    printlevel=$printlevel
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
+    ]]></command>
+    <inputs>
+        <param argument="biom" type="data" format="biom1" label="Biom input dataset"/>
+        <!-- TODO: read label options from biom file -->
+        <param argument="label" type="text" value="userLabel" label="label - OTU Labels"
+            help="Enter a distance label to be used in the shared file created from your biom file (e.g. 0.03)"/>
+        <param argument="basis" type="select" label="Summary type"
+            help="indicate what you want the summary file to represent, options are otu and sequence. Default is otu.
+            For example consider the following basis=sequence could give Clostridiales 3 105, where 105 is the total
+            number of sequences whose otu classified to Clostridiales. Now for basis=otu could give Clostridiales 3 7,
+            where 7 is the number of otus that classified to Clostridiales. ">
+            <option value="otu" selected="true">OTU</option>
+            <option value="sequence">Sequence</option>
+        </param>
+        <param argument="relabund" type="boolean" truevalue="T" falsevalue="F" label="Relative abundance values"
+            help="use relative abundances rather than raw abundances for the tax.summary file"/>
+        <expand macro="param-output"/>
+        <expand macro="param-printlevel"/>
+        <expand macro="param-savelog"/>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <data name="shared" format="mothur.shared" from_work_dir="input*.shared" label="${tool.name} on ${on_string}: shared"/>
+        <data name="taxonomy" format="mothur.cons.taxonomy" from_work_dir="input*.cons.taxonomy" label="${tool.name} on ${on_string}: cons.taxonomy"/>
+        <data name="tax.summary" format="mothur.tax.summary" from_work_dir="input*.tax.summary" label="${tool.name} on ${on_string}: tax.summary"/>
+    </outputs>
+    <tests>
+        <test><!-- test with biom without metadata -->
+            <param name="biom" value="samplebiom.biom1"/>
+            <output name="shared" ftype="mothur.shared">
+                <assert_contents>
+                    <expand macro="test-shared-format"/>
+                </assert_contents>
+            </output>
+            <param name="savelog" value="true"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!-- test with biom file with metadata -->
+            <param name="biom" value="example.biom"/>
+            <output name="shared" ftype="mothur.shared">
+                <assert_contents>
+                    <expand macro="test-shared-format"/>
+                </assert_contents>
+            </output>
+            <output name="taxonomy" ftype="mothur.cons.taxonomy">
+                <assert_contents>
+                    <expand macro="test-taxonomy-format"/>
+                    <has_text text="GG_OTU_1"/>
+                </assert_contents>
+            </output>
+            <output name="tax.summary" ftype="mothur.tax.summary">
+                <assert_contents>
+                    <expand macro="test-taxsummary-format"/>
+                </assert_contents>
+            </output>
+            <param name="savelog" value="true"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!-- test with some more parameters -->
+            <param name="biom" value="example.biom"/>
+            <param name="label" value="0.03"/>
+            <param name="output" value="detail"/>
+            <param name="basis" value="sequence"/>
+            <param name="printlevel" value="4"/>
+            <output name="shared" ftype="mothur.shared">
+                <assert_contents>
+                    <expand macro="test-shared-format"/>
+                </assert_contents>
+            </output>
+            <output name="taxonomy" ftype="mothur.cons.taxonomy">
+                <assert_contents>
+                    <expand macro="test-taxonomy-format"/>
+                    <has_text text="GG_OTU_1"/>
+                </assert_contents>
+            </output>
+            <output name="tax.summary" ftype="mothur.tax.summary">
+                <assert_contents>
+                    <expand macro="test-taxsummary-format"/>
+                    <has_text text="Euryarchaeota"/>
+                </assert_contents>
+            </output>
+            <param name="savelog" value="true"/>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documentation**
+
+The biom.info command reads a biom file creates a shared file. If your biom file contains metadata mothur will also
+create taxonomy or constaxonomy along with tax.summary files.
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>