diff chimera.perseus.xml @ 0:35c11001da8b 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/chimera.perseus.xml	Fri May 19 05:29:15 2017 -0400
@@ -0,0 +1,74 @@
+<tool profile="16.07" id="mothur_chimera_perseus" name="Chimera.perseus" version="@WRAPPER_VERSION@.0">
+    <description>Find putative chimeras using chimeraCheck</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 "$fasta" fasta.dat &&
+        ln -s "$name" name.dat &&
+        ln -s "$group" group.dat &&
+
+        echo 'chimera.perseus(
+            fasta=fasta.dat,
+            #if $name.is_of_type("mothur.names"):
+                name=name.dat,
+            #elif $name.is_of_type("mothur.count_table"):
+                count=name.dat,
+            #end if
+            #if $group:
+                group=group.dat,
+            #end if
+            alpha=$alpha,
+            beta=$beta,
+            cutoff=$cutoff,
+            dereplicate=$dereplicate,
+            processors='\${GALAXY_SLOTS:-8}'
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+        | tee mothur.out.log
+    ]]></command>
+    <inputs>
+        <param name="fasta" type="data" format="mothur.align" label="fasta - Candiate Aligned Sequences"/>
+        <param name="name" type="data" format="mothur.names,mothur.count_table" label="name - Names or count_table"/>
+        <param name="group" type="data" format="mothur.groups" optional="true" label="group - Sequences Name reference"/>
+        <param name="alpha" type="float" value="-5.54" label="alpha" help="The default is -5.54"/>
+        <param name="beta" type="float" value="0.33" label="beta" help="The default is 0.33"/>
+        <param name="cutoff" type="float" value="0.50" label="cutoff" help="The default is 0.50"/>
+        <param name="dereplicate" type="boolean" falsevalue="false" truevalue="true" checked="false" label="dereplicate - remove chimeric sequences from all groups" help="If parameter is false, then if one group finds the seqeunce to be chimeric, then all groups find it to be chimeric. default=false"/>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <data name="out_chimeras" format="tabular" from_work_dir="fasta.perseus.chimeras" label="${tool.name} on ${on_string}: perseus.chimeras"/>
+        <data name="out_accnos" format="mothur.accnos" from_work_dir="fasta.perseus.accnos" label="${tool.name} on ${on_string}: perseus.accnos"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="fasta" value="amazon.fasta" ftype="fasta"/>
+            <param name="name" value="amazon1.names" ftype="mothur.names"/>
+            <output name="out_chimeras" md5="bcd513127321a32035764a2087c23528" ftype="tabular"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <!-- TODO: find/create test dataset with chimera present -->
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documentation**
+
+The chimera.perseus_ command reads a fasta and name file, and outputs potentially chimeric sequences.
+
+.. _chimera.perseus: https://www.mothur.org/wiki/Chimera.perseus
+
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>