diff cluster.fragments.xml @ 0:145595c55727 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/cluster.fragments.xml	Fri May 19 05:26:17 2017 -0400
@@ -0,0 +1,68 @@
+<tool profile="16.07" id="mothur_cluster_fragments" name="Cluster.fragments" version="@WRAPPER_VERSION@.0">
+    <description> Group sequences that are part of a larger sequence</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 "$fasta" fasta.dat &&
+        ln -s "$names" names.dat &&
+        ln -s "$count" count.dat &&
+
+        echo 'cluster.fragments(
+            fasta=fasta.dat,
+            diffs=$diffs,
+            percent=$percent,
+            #if $count:
+                count=count.dat,
+            #end if
+            name=names.dat
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+        | tee mothur.out.log
+    ]]></command>
+    <inputs>
+        <param name="fasta" type="data" format="fasta" label="fasta - Sequences to filter"/>
+        <param name="names" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
+        <param name="diffs" type="integer" value="0" label="diffs - Number of mismatched bases to allow between sequences in a group (default 0)" min="0"/>
+        <param name="percent" type="integer" value="0" label="percent - percentage of differences allowed ( between 1 and 100, default 0)" min="0" max="100"
+               help="The percent parameter allows you to set percentage of differences allowed, default=0. percent=2 means if the number of difference is less than or equal to two percent of the length of the fragment, then cluster. You may use diffs and percent at the same time to say something like: If the number or differences is greater than 1 or more than 2% of the fragment length, don't merge."/>
+        <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <data name="out_fasta" format_source="fasta" from_work_dir="fasta*.fragclust.fasta" label="${tool.name} on ${on_string}: fasta"/>
+        <data name="out_names" format="mothur.names" from_work_dir="fasta*.fragclust.names" label="${tool.name} on ${on_string}: names"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="fasta" value="amazon.fasta" ftype="fasta"/>
+            <param name="names" value="amazon1.names" ftype="mothur.names"/>
+            <output name="out_fasta" file="amazon.fragclust.fasta" ftype="fasta"/>
+            <output name="out_names" file="amazon.fragclust.names" ftype="mothur.names"/>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documentation**
+
+The cluster.fragments_ command groups sequences that are part of a larger sequence.
+
+.. _cluster.fragments: https://www.mothur.org/wiki/Cluster.fragments
+
+v1.21: Updated to Mothur 1.33. Added count parameter.
+
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>