diff bin.seqs.xml @ 3:82c917a4ed55 draft

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

--- a/bin.seqs.xml	Fri Sep 08 14:29:17 2017 -0400
+++ b/bin.seqs.xml	Tue Mar 20 22:07:19 2018 -0400
@@ -7,44 +7,46 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$name" name.dat &&
-        ln -s "$group" group.dat &&
-        ln -s "$fasta" fasta.dat &&
-        ln -s "$otu" otu.dat &&
-        ln -s "$count" count.dat &&
+## create symlinks to input datasets
+ln -s '$name' name.dat &&
+ln -s '$group' group.dat &&
+ln -s '$fasta' fasta.dat &&
+ln -s '$otu' otu.dat &&
+ln -s '$count' count.dat &&
 
-        echo 'bin.seqs(
-            #if $name:
-                name=name.dat,
-            #end if
-            #if $group:
-                group=group.dat,
-            #end if
-            #if $label:
-                label=${ str($label).replace(",","-") },
-            #end if
-            #if $count:
-                count=count.dat,
-            #end if
-            fasta=fasta.dat,
-            list=otu.dat
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'bin.seqs(
+    #if $name:
+        name=name.dat,
+    #end if
+    #if $group:
+        group=group.dat,
+    #end if
+    #if $label:
+        label=${ str($label).replace(",","-") },
+    #end if
+    #if $count:
+        count=count.dat,
+    #end if
+    fasta=fasta.dat,
+    list=otu.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 Bin"/>
-        <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
-        <param name="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
-        <param name="label" type="select" label="label - OTU Labels" multiple="true">
+        <param argument="fasta" type="data" format="fasta" label="fasta - Sequences to Bin"/>
+        <param argument="list" name="otu" type="data" format="mothur.list" label="list - OTU List"/>
+        <param argument="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
+        <param argument="label" type="select" multiple="true" label="label - OTU Labels">
             <expand macro="labeloptions"/>
         </param>
-        <param name="group" type="data" format="mothur.groups" optional="true" label="group - Sequences Name reference"/>
-        <param name="count" type="data" format="mothur.count_table" optional="true" label="count - Represents the number of duplicate sequences for a given representitive sequence"/>
+        <param argument="group" type="data" format="mothur.groups" optional="true" label="group - Sequences Name reference"/>
+        <param argument="count" type="data" format="mothur.count_table" optional="true" label="count - Count Table"
+            help="Represents the number of duplicate sequences for a given representitive sequence"/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -57,8 +59,14 @@
             <param name="otu" value="amazon.an.list"/>
             <param name="fasta" value="amazon.fasta"/>
             <output_collection name="fastafiles" count="36">
-                <element name="0.22" md5="8fd8dd141561dc3e574e0c3f356e7e84" ftype="fasta"/>
+                <element name="0.22" ftype="fasta">
+                    <assert_contents>
+                        <expand macro="test-fasta-format"/>
+                        <has_text text="U68589"/>
+                    </assert_contents>
+                </element>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with group and name file and label select -->
@@ -68,23 +76,30 @@
             <param name="group" value="amazon.groups" ftype="mothur.groups"/>
             <param name="label" value="0.03,0.05,0.22"/>
             <output_collection name="fastafiles" count="3">
-                <element name="0.22" md5="02755d06b535fdcdb5a70b6eb767d1f6" ftype="fasta"/>
+                <element name="0.22" ftype="fasta">
+                    <assert_contents>
+                        <expand macro="test-fasta-format"/>
+                        <has_text text="U68589"/>
+                    </assert_contents>
+                </element>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
 **Command Documentation**
 
-The bin.seqs_ command generates fasta-formatted files where sequences are ordered according to the OTU from the list_file_ that they belong to. Such an output may be helpful for generating primers specific to an OTU or for classification of sequences.
+The bin.seqs_ command generates fasta-formatted files where sequences are ordered according to the OTU
+from the list_file_ that they belong to. Such an output may be helpful for generating primers specific
+to an OTU or for classification of sequences.
 
 .. _list_file: https://www.mothur.org/wiki/List_file
 .. _bin.seqs: https://www.mothur.org/wiki/Bin.seqs
-]]>
-    </help>
+
+    ]]></help>
     <expand macro="citations"/>
 </tool>