diff list.seqs.xml @ 0:24044cd8ef87 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/list.seqs.xml	Fri May 19 05:39:09 2017 -0400
@@ -0,0 +1,114 @@
+<tool profile="16.07" id="mothur_list_seqs" name="List.seqs" version="@WRAPPER_VERSION@.0">
+    <description>Lists the names (accnos) of the sequences</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 "$search.input" search.input.dat &&
+
+        echo 'list.seqs(
+            #if $search.intype == "fasta":
+                fasta=search.input.dat
+            #elif $search.intype == "fastq":
+                fastq=search.input.dat
+            #elif $search.intype == "name":
+                name=search.input.dat
+            #else if $search.intype == "group":
+                group=search.input.dat
+            #elif $search.intype == "alignreport":
+                alignreport=search.input.dat
+            #elif $search.intype == "list":
+                list=search.input.dat
+            #elif $search.intype == "taxonomy":
+                taxonomy=search.input.dat
+            #elif $search.intype == "count":
+                count=search.input.dat
+            #end if
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+        | tee mothur.out.log
+    ]]></command>
+    <inputs>
+        <conditional name="search">
+            <param name="intype" type="select" label="Type to list" help="">
+                <option value="fasta">Sequence Fasta</option>
+                <option value="fastq">Sequence Fastq</option>
+                <option value="name">Sequences Name reference</option>
+                <option value="group">Groups</option>
+                <option value="alignreport">Align Report</option>
+                <option value="list">OTU List</option>
+                <option value="taxonomy">Sequence Taxonomy</option>
+                <option value="count">Count Table</option>
+            </param>
+            <when value="fasta">
+                <param name="input" type="data" format="fasta" label="fasta - Fasta"/>
+            </when>
+            <when value="fastq">
+                <param name="input" type="data" format="fastq" label="fasta - Fasta"/>
+            </when>
+            <when value="name">
+                <param name="input" type="data" format="mothur.names" label="name - Names"/>
+            </when>
+            <when value="group">
+                <param name="input" type="data" format="mothur.groups" label="group - Groups"/>
+            </when>
+            <when value="alignreport">
+                <param name="input" type="data" format="mothur.align.report" label="alignreport - Align Report"/>
+            </when>
+            <when value="list">
+                <param name="input" type="data" format="mothur.list" label="list - OTU List"/>
+            </when>
+            <when value="taxonomy">
+                <param name="input" type="data" format="mothur.seq.taxonomy" label="taxonomy - Sequence Taxonomy"/>
+            </when>
+            <when value="count">
+                <param name="input" type="data" format="mothur.count_table" label="count - Count Table"/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <data name="out_file" format="mothur.accnos" from_work_dir="search.input*.accnos" label="${tool.name} on ${on_string}: accnos"/>
+    </outputs>
+    <tests>
+        <test><!-- test with fasta -->
+            <param name="intype" value="fasta"/>
+            <param name="input" value="amazon.fasta"/>
+            <output name="out_file" md5="590f62ce757219c2e137a532fcd814d1" ftype="mothur.accnos"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!-- test with count file -->
+            <param name="intype" value="count"/>
+            <param name="input" value="amazon.count_table"/>
+            <output name="out_file" md5="360dfea2de2da4d55e75071b026c83b6" ftype="mothur.accnos"/>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documentation**
+
+The list.seqs_ command writes out the names of the sequences found within a fasta, name_, group_, list_, align.report_ or taxonomy_ file.
+
+.. _name: https://www.mothur.org/wiki/Name_file
+.. _group: https://www.mothur.org/wiki/Group_file
+.. _list: https://www.mothur.org/wiki/List_file
+.. _align.report: https://www.mothur.org/wiki/Align.seqs
+.. _taxonomy: https://www.mothur.org/wiki/Taxonomy_outline
+.. _list.seqs: https://www.mothur.org/wiki/list.seqs
+
+v.1.20.0: Updated to mothur 1.33, added count and fastq option
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>