mothur_get_lineage: get.lineage.xml comparison

comparison get.lineage.xml @ 2:c5034189eb03 draft

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

author	iuc
date	Tue, 20 Mar 2018 22:27:20 -0400
parents	f217eb7fad54
children	6fbd83d3a29f

comparison

equal deleted inserted replaced

-:0aea19572961
+:c5034189eb03
 </macros>
 <expand macro="requirements"/>
 <expand macro="stdio"/>
 <expand macro="version_command"/>
 <command><![CDATA[
 @SHELL_OPTIONS@
 #import re
 ## create symlinks to input datasets
-ln -s "$file.taxonomy" file.taxonomy.dat &&
+ln -s '$file.taxonomy' file.taxonomy.dat &&
 #if $file.filetype == "useconstaxonomy":
-ln -s "$file.shared" file.shared.dat &&
+ln -s '$file.shared' file.shared.dat &&
-ln -s "$file.list" file.list.dat &&
+ln -s '$file.list' file.list.dat &&
+#end if
+ln -s '$fasta_in' fasta_in.dat &&
+ln -s '$group_in' group_in.dat &&
+ln -s '$alignreport_in' alignreport_in.dat &&
+ln -s '$list_in' list_in.dat &&
+ln -s '$name_in' name_in.dat &&
+ln -s '$count' count.dat &&
+echo 'get.lineage(
+#if $file.filetype == "usetaxonomy":
+taxonomy=file.taxonomy.dat
+#else
+constaxonomy=file.taxonomy.dat
+#if $file.shared:
+,shared=file.shared.dat
 #end if
-ln -s "$fasta_in" fasta_in.dat &&
+#if $file.list:
-ln -s "$group_in" group_in.dat &&
+,list=file.list.dat
-ln -s "$alignreport_in" alignreport_in.dat &&
+#end if
-ln -s "$list_in" list_in.dat &&
+#end if
-ln -s "$name_in" name_in.dat &&
+#if $file.taxons:
-ln -s "$count" count.dat &&
+#set taxonstring=str($file.taxons).replace(",","-")
+,taxon='"'$re.sub("(\s|,)+",",",$re.sub("\(\d+\)","", $taxonstring ))'"'
-echo 'get.lineage(
+#elif $taxon:
-#if $file.filetype == "usetaxonomy":
+,taxon='"'$re.sub("(\s|,)+",",",$re.sub("\(\d+\)","", $taxon.value )).replace(",","-")'"'
-taxonomy=file.taxonomy.dat
+#end if
-#else
+#if $fasta_in:
-constaxonomy=file.taxonomy.dat
+,fasta=fasta_in.dat
-#if $file.shared:
+#end if
-,shared=file.shared.dat
+#if $group_in:
-#end if
+,group=group_in.dat
-#if $file.list:
+#end if
-,list=file.list.dat
+#if $alignreport_in:
-#end if
+,alignreport=alignreport_in.dat
 #end if
-#if $file.taxons:
+#if $list_in:
-#set taxonstring=str($file.taxons).replace(",","-")
+,list=list_in.dat
-,taxon='"'$re.sub("(\s|,)+",",",$re.sub("\(\d+\)","", $taxonstring ))'"'
+#end if
-#elif $taxon:
+#if $name_in:
-,taxon='"'$re.sub("(\s|,)+",",",$re.sub("\(\d+\)","", $taxon.value )).replace(",","-")'"'
+,name=name_in.dat
-#end if
+,dups=$dups
-#if $fasta_in:
+#end if
-,fasta=fasta_in.dat
+#if $count:
-#end if
+,count=count.dat
-#if $group_in:
+#end if
-,group=group_in.dat
+)'
-#end if
+| sed 's/ //g'  ## mothur trips over whitespace
-#if $alignreport_in:
+| mothur
-,alignreport=alignreport_in.dat
+| tee mothur.out.log
-#end if
-#if $list_in:
-,list=list_in.dat
-#end if
-#if $name_in:
-,name=name_in.dat
-,dups=$dups
-#end if
-#if $count:
-,count=count.dat
-#end if
-)'
-| sed 's/ //g'  ## mothur trips over whitespace
-| mothur
-| tee mothur.out.log
 ]]></command>
 <inputs>
 <conditional name="file">
 <param name="filetype" type="select" label="choose which file is used">
 <option value="usetaxonomy" selected="true">taxonomy</option>
 </valid>
 </sanitizer>
 </param>
 </when>
 <when value="useconstaxonomy">
-<param name="taxonomy" type="data" format="mothur.cons.taxonomy" label="constaxonomy - Constaxonomy file. Provide either a constaxonomy file or a taxonomy file" help="please make sure your file has no quotation marks in it"/>
+<param name="taxonomy" type="data" format="mothur.cons.taxonomy" label="constaxonomy - Constaxonomy file. Provide either a constaxonomy file or a taxonomy file"
+help="please make sure your file has no quotation marks in it"/>
 <param name="taxons" type="select" size="120" optional="true" multiple="true" label="Browse Taxons from Taxonomy">
 <options from_dataset="taxonomy">
 <column name="name" index="2"/>
 <column name="value" index="2"/>
 <filter type="unique_value" name="unique_taxon" column="2"/>
 </param>
 <param name="shared" type="data" format="mothur.shared" optional="true" label="shared - shared file"/>
 <param name="list" type="data" format="mothur.list" optional="true" label="list - list file"/>
 </when>
 </conditional>
-<param name="taxon" type="text" area="True" size="5x120" label="taxon - Manually select Taxons for filtering" help="If no taxons selected from file, Enter 1 or more taxons separated by dashes here, e.g. Bacteria;Firmicutes;-Bacteria;Actinobacteria; "/>
+<param name="taxon" type="text" area="True" size="5x120" label="taxon - Manually select Taxons for filtering"
+help="If no taxons selected from file, Enter 1 or more taxons separated by dashes here, e.g. Bacteria;Firmicutes;-Bacteria;Actinobacteria; "/>
 <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - Fasta Sequences"/>
 <param name="group_in" type="data" format="mothur.groups" optional="true" label="group - Groups"/>
 <param name="alignreport_in" type="data" format="mothur.align.report" optional="true" label="alignreport - Align Report"/>
 <param name="list_in" type="data" format="mothur.list" optional="true" label="list - OTU List"/>
 <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
 <param name="dups" type="boolean" truevalue="true" falsevalue="false" checked="true" label="dups - Apply to duplicate names"/>
-<param name="count" type="data" format="mothur.count_table" optional="true" help="The count file is similar to the name file in that it is used to represent the number of duplicate sequences for a given representative sequence. It can also contain group information"/>
+<param name="count" type="data" format="mothur.count_table" optional="true"  label="Count Table"
+help="The count file is similar to the name file in that it is used to represent the number of duplicate sequences for a given representative sequence. It can also contain group information"/>
+<expand macro="param-savelog"/>
 </inputs>
 <outputs>
 <expand macro="logfile-output"/>
 <data name="taxonomy_out" format="mothur.seq.taxonomy" from_work_dir="file.taxonomy*.pick.*" label="${tool.name} on ${on_string}: pick.taxonomy"/>
 <data name="fasta_out" format_source="fasta_in" from_work_dir="fasta_in*.pick.*" label="${tool.name} on ${on_string}: pick.fasta">
 <param name="taxonomy" value="example.constaxonomy" ftype="mothur.cons.taxonomy"/>
 <param name="taxons" value="Bacteria(100);Firmicutes(100);Clostridia(70);Clostridiales(70);Lachnospiraceae(51);unclassified;,Bacteria(100);Proteobacteria(100);Gammaproteobacteria(100);unclassified;unclassified;unclassified;"/>
 <output name="taxonomy_out" md5="0ea2511f40073a95c0812268da0cf727"/>
 </test>
 </tests>
-<help>
+<help><![CDATA[
-<![CDATA[
 @MOTHUR_OVERVIEW@
 **Command Documentation**
 .. _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
 .. _get.lineage: https://www.mothur.org/wiki/Get.lineage
-]]>
+]]></help>
-</help>
 <expand macro="citations"/>
 </tool>

Mercurial > repos > iuc > mothur_get_lineage

comparison get.lineage.xml @ 2:c5034189eb03 draft