mothur_sub_sample: sub.sample.xml comparison

comparison sub.sample.xml @ 2:46d13e8c60ba draft

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

author	iuc
date	Tue, 20 Mar 2018 22:24:53 -0400
parents	be6c106b1960
children	2986f7b01e74

comparison

equal deleted inserted replaced

-:e866e31f6da3
+:46d13e8c60ba
 </macros>
 <expand macro="requirements"/>
 <expand macro="stdio"/>
 <expand macro="version_command"/>
 <command><![CDATA[
 @SHELL_OPTIONS@
 ## create symlinks to input datasets
-ln -s "$input.otu" input_otu.dat &&
+ln -s '$input.otu' input_otu.dat &&
-ln -s "$count" count.dat &&
+ln -s '$count' count.dat &&
-ln -s "$taxonomy" taxonomy.dat &&
+ln -s '$taxonomy' taxonomy.dat &&
 #if $input.format == "fasta":
-ln -s "$input.name_in" input_name_in.dat &&
+ln -s '$input.name_in' input_name_in.dat &&
+#end if
+#if ($input.format == "fasta" or $input.format == "list") and $input.use_group.to_filter == "yes":
+ln -s '$input.use_group.group_in' input_use_group_group_in.dat &&
+#end if
+echo 'sub.sample(
+#if $input.format == "fasta":
+fasta=input_otu.dat
+#if $input.name_in:
+,name=input_name_in.dat
 #end if
-#if ($input.format == "fasta" or $input.format == "list") and $input.use_group.to_filter == "yes":
+#else
-ln -s "$input.use_group.group_in" input_use_group_group_in.dat &&
+#if $input.format == "list":
+list=input_otu.dat
+#elif $input.format == "sabund":
+sabund=input_otu.dat
+#elif $input.format == "rabund":
+rabund=input_otu.dat
+#elif $input.format == "shared":
+shared=input_otu.dat
+#if $input.groups:
+,groups=${ str($input.groups).replace(",","-") }
+#end if
 #end if
+#if $input.label:
-echo 'sub.sample(
+,label=${ str($input.label).replace(",","-") }
-#if $input.format == "fasta":
+#end if
-fasta=input_otu.dat
+#end if
-#if $input.name_in:
+#if $input.format == "fasta" or $input.format == "list":
-,name=input_name_in.dat
+#if $input.use_group.to_filter == "yes":
-#end if
+,group=input_use_group_group_in.dat
-#else
+#if $input.use_group.groups:
-#if $input.format == "list":
+,groups=${ str($input.use_group.groups).replace(",","-") }
-list=input_otu.dat
-#elif $input.format == "sabund":
-sabund=input_otu.dat
-#elif $input.format == "rabund":
-rabund=input_otu.dat
-#elif $input.format == "shared":
-shared=input_otu.dat
-#if $input.groups:
-,groups=${ str($input.groups).replace(",","-") }
-#end if
-#end if
-#if $input.label:
-,label=${ str($input.label).replace(",","-") }
-#end if
 #end if
-#if $input.format == "fasta" or $input.format == "list":
+,persample=$input.use_group.persample
-#if $input.use_group.to_filter == "yes":
+#end if
-,group=input_use_group_group_in.dat
+#end if
-#if $input.use_group.groups:
+#if $count:
-,groups=${ str($input.use_group.groups).replace(",","-") }
+,count=count.dat
 #end if
-,persample=$input.use_group.persample
+#if $taxonomy:
-#end if
+,taxonomy=taxonomy.dat
 #end if
-#if $count:
+#if $size:
-,count=count.dat
+,size=$size
 #end if
-#if $taxonomy:
+)'
-,taxonomy=taxonomy.dat
+| sed 's/ //g'  ## mothur trips over whitespace
-#end if
+| mothur
-#if $size:
+| tee mothur.out.log
-,size=$size
-#end if
-)'
-| sed 's/ //g'  ## mothur trips over whitespace
-| mothur
-| tee mothur.out.log
 ]]></command>
 <inputs>
 <conditional name="input">
 <param name="format" type="select" label="Select type of data to sub sample">
 <option value="fasta">FASTA</option>
 </when>
 </conditional>
 <param name="size" type="integer" value="" min="1" optional="true" label="size - If set, the number of samples to pick"/>
 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
 <param name="taxonomy" type="data" format="mothur.seq.taxonomy,mothur.ref.taxonomy" optional="true" label="taxonomy - allows a taxonomy file"/>
+<expand macro="param-savelog"/>
 </inputs>
 <outputs>
 <expand macro="logfile-output"/>
 <data name="fasta_out" format_source="otu" from_work_dir="input_otu*.subsample.*" label="${tool.name} on ${on_string}: subsample.fasta">
 <filter>input['format'] == 'fasta'</filter>
 <has_text text="label"/>
 <has_text text="numOtus"/>
 </assert_contents>
 </element>
 </output_collection>
+<param name="savelog" value="true"/>
 <expand macro="logfile-test"/>
 </test>
 <test><!-- test with list and group file and label select-->
 <param name="format" value="list"/>
 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
 <has_text text="label"/>
 <has_text text="numOtus"/>
 </assert_contents>
 </element>
 </output_collection>
+<param name="savelog" value="true"/>
 <expand macro="logfile-test"/>
 </test>
 <test><!-- test with fasta and taxonomy -->
 <param name="format" value="fasta"/>
 <param name="otu" value="amazon.fasta" ftype="fasta"/>
 <output name="taxonomy_out" ftype="mothur.seq.taxonomy">
 <assert_contents>
 <has_line_matching expression="^U[0-9]+\tBacteria.*$"/>
 </assert_contents>
 </output>
+<param name="savelog" value="true"/>
 <expand macro="logfile-test"/>
 </test>
 <test><!-- test with fasta and group file and name file -->
 <param name="format" value="fasta"/>
 <param name="otu" value="amazon.fasta" ftype="fasta"/>
 <output name="names_out" ftype="mothur.names">
 <assert_contents>
 <has_line_matching expression="^U[0-9]+\tU[0-9]+$"/>
 </assert_contents>
 </output>
+<param name="savelog" value="true"/>
 <expand macro="logfile-test"/>
 </test>
 <test><!-- test with shared -->
 <param name="format" value="shared"/>
 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
 <has_text text="forest"/>
 <not_has_text text="pasture"/>
 </assert_contents>
 </element>
 </output_collection>
+<param name="savelog" value="true"/>
 <expand macro="logfile-test"/>
 </test>
 <test><!-- test with rabund -->
 <param name="format" value="rabund"/>
 <param name="otu" value="amazon.an.rabund" ftype="mothur.rabund"/>
 <assert_contents>
 <has_text text="unique"/>
 <has_text text="0.55"/>
 </assert_contents>
 </output>
+<param name="savelog" value="true"/>
 <expand macro="logfile-test"/>
 </test>
 <test><!-- test with sabund -->
 <param name="format" value="sabund"/>
 <param name="otu" value="amazon.an.sabund" ftype="mothur.sabund"/>
 <assert_contents>
 <has_text text="unique"/>
 <has_text text="0.55"/>
 </assert_contents>
 </output>
+<param name="savelog" value="true"/>
 <expand macro="logfile-test"/>
 </test>
 </tests>
-<help>
+<help><![CDATA[
-<![CDATA[
 @MOTHUR_OVERVIEW@
 **Command Documentation**
 .. _shared: https://www.mothur.org/wiki/Shared_file
 .. _rabund: https://www.mothur.org/wiki/Rabund_file
 .. _sabund: https://www.mothur.org/wiki/Sabund_file
 .. _sub.sample: https://www.mothur.org/wiki/Sub.sample
-]]>
+]]></help>
-</help>
 <expand macro="citations"/>
 </tool>

Mercurial > repos > iuc > mothur_sub_sample

comparison sub.sample.xml @ 2:46d13e8c60ba draft