diff get.seqs.xml @ 2:5acd4d7339b9 draft

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

--- a/get.seqs.xml	Tue Sep 05 16:53:01 2017 -0400
+++ b/get.seqs.xml	Tue Mar 20 21:55:58 2018 -0400
@@ -7,54 +7,54 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$accnos" accnos.dat &&
-        ln -s "$fasta_in" fasta_in.dat &&
-        ln -s "$fastq_in" fastq_in.dat &&
-        ln -s "$count_in" count_in.dat &&
-        ln -s "$qfile_in" qfile_in.dat &&
-        ln -s "$name_in" name_in.dat &&
-        ln -s "$group_in" group_in.dat &&
-        ln -s "$alignreport_in" alignreport_in.dat &&
-        ln -s "$list_in" list_in.dat &&
-        ln -s "$taxonomy_in" taxonomy_in.dat &&
+## create symlinks to input datasets
+ln -s '$accnos' accnos.dat &&
+ln -s '$fasta_in' fasta_in.dat &&
+ln -s '$fastq_in' fastq_in.dat &&
+ln -s '$count_in' count_in.dat &&
+ln -s '$qfile_in' qfile_in.dat &&
+ln -s '$name_in' name_in.dat &&
+ln -s '$group_in' group_in.dat &&
+ln -s '$alignreport_in' alignreport_in.dat &&
+ln -s '$list_in' list_in.dat &&
+ln -s '$taxonomy_in' taxonomy_in.dat &&
 
-        echo 'get.seqs(
-            accnos=accnos.dat,
-            #if $fasta_in:
-                fasta=fasta_in.dat,
-            #end if
-            #if $fastq_in:
-                fastq=fastq_in.dat,
-            #end if
-            #if $count_in:
-                count=count_in.dat,
-            #end if
-            #if $qfile_in:
-                qfile=qfile_in.dat,
-            #end if
-            #if $name_in:
-                name=name_in.dat,
-            #end if
-            #if $group_in:
-                group=group_in.dat,
-            #end if
-            #if $alignreport_in:
-                alignreport=alignreport_in.dat,
-            #end if
-            #if $list_in:
-                list=list_in.dat,
-            #end if
-            #if $taxonomy_in:
-                taxonomy=taxonomy_in.dat,
-            #end if
-            dups=$dups
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'get.seqs(
+    accnos=accnos.dat,
+    #if $fasta_in:
+        fasta=fasta_in.dat,
+    #end if
+    #if $fastq_in:
+        fastq=fastq_in.dat,
+    #end if
+    #if $count_in:
+        count=count_in.dat,
+    #end if
+    #if $qfile_in:
+        qfile=qfile_in.dat,
+    #end if
+    #if $name_in:
+        name=name_in.dat,
+    #end if
+    #if $group_in:
+        group=group_in.dat,
+    #end if
+    #if $alignreport_in:
+        alignreport=alignreport_in.dat,
+    #end if
+    #if $list_in:
+        list=list_in.dat,
+    #end if
+    #if $taxonomy_in:
+        taxonomy=taxonomy_in.dat,
+    #end if
+    dups=$dups
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="accnos" type="data" format="mothur.accnos" label="accnos - Accession Names"/>
@@ -68,6 +68,7 @@
         <param name="list_in" type="data" format="mothur.list" optional="true" label="list - OTU List"/>
         <param name="taxonomy_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/>
         <param name="dups" type="boolean" truevalue="dups" falsevalue="false" checked="true" label="dups - Apply to duplicates"/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -105,12 +106,14 @@
             <param name="fasta_in" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/>
             <param name="dups" value=""/>
             <output name="fasta_out" md5="f9335b6b70dc639e420d33809e51431d"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test>
             <param name="accnos" value="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos"/>
             <param name="fastq_in" value="Mock_S280_L001_R1_001_small.fastq"/>
-            <output name="fastq_out" md5="e9aae546bf9c00cb7e884dff267d4ba1"/>
+            <output name="fastq_out" md5="81d026f969e15b8c8701f8dc5f3a6904"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test>
@@ -120,18 +123,19 @@
             <param name="fastq_in" value="Mock_S280_L001_R1_001_small.fastq"/>
             <param name="dups" value="false"/>
             <output name="fasta_out" md5="f9335b6b70dc639e420d33809e51431d"/>
-            <output name="fastq_out" md5="e9aae546bf9c00cb7e884dff267d4ba1"/>
+            <output name="fastq_out" md5="81d026f969e15b8c8701f8dc5f3a6904"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test>
             <param name="accnos" value="amazon.bad.accnos"/>
             <param name="count_in" value="amazon.count_table"/>
             <output name="count_out" md5="6892dd99850ce9e9f8f15e77b28f57e2"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -148,7 +152,7 @@
 .. _get.seqs: https://www.mothur.org/wiki/Get.seqs
 
 v.1.27.0 : Updated to Mothur 1.33, added count and fastq params
-]]>
-    </help>
+
+    ]]></help>
     <expand macro="citations"/>
 </tool>