mothur_get_groups: get.groups.xml comparison

comparison get.groups.xml @ 3:378f8103cf1b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4

author	iuc
date	Wed, 14 Feb 2018 10:12:03 -0500
parents	1e6a7d59a872
children	3d777453d29d

comparison

equal deleted inserted replaced

-:40561fdfb8d3
+:378f8103cf1b
 </macros>
 <expand macro="requirements"/>
 <expand macro="stdio"/>
 <expand macro="version_command"/>
 <command><![CDATA[
 @SHELL_OPTIONS@
 ## create symlinks to input datasets
-ln -s "$group_in" group_in.dat &&
+ln -s '$group_in' group_in.dat &&
-ln -s "$fasta_in" fasta_in.dat &&
+ln -s '$fasta_in' fasta_in.dat &&
-ln -s "$name_in" name_in.dat &&
+ln -s '$name_in' name_in.dat &&
-ln -s "$list_in" list_in.dat &&
+ln -s '$list_in' list_in.dat &&
-ln -s "$shared_in" shared_in.dat &&
+ln -s '$shared_in' shared_in.dat &&
-ln -s "$taxonomy_in" taxonomy_in.dat &&
+ln -s '$taxonomy_in' taxonomy_in.dat &&
-ln -s "$design_in" design_in.dat &&
+ln -s '$design_in' design_in.dat &&
-#if $groupnames.source == 'accnos':
+ln -s '$column_in' column_in.dat &&
-ln -s "$groupnames.accnos" groupnames.accnos.dat &&
+ln -s '$phylip_in' phylip_in.dat &&
+#if $groupnames.source == 'accnos':
+ln -s '$groupnames.accnos' groupnames.accnos.dat &&
+#end if
+echo 'get.groups(
+#if $group_in.is_of_type("mothur.groups"):
+group=group_in.dat
+#else
+count=group_in.dat
+#end if
+#if $groupnames.source == 'groups':
+#if $groupnames.groups:
+,groups=${ str($groupnames.groups).replace(",","-") }
 #end if
+#else
-echo 'get.groups(
+,accnos=groupnames.accnos.dat
-#if $group_in.is_of_type("mothur.groups"):
+#end if
-group=group_in.dat
+#if $fasta_in:
-#else
+,fasta=fasta_in.dat
-count=group_in.dat
+#end if
-#end if
+#if $name_in:
-#if $groupnames.source == 'groups':
+,name=name_in.dat
-#if $groupnames.groups:
+#end if
-,groups=${ str($groupnames.groups).replace(",","-") }
+#if $list_in:
-#end if
+,list=list_in.dat
-#else
+#end if
-,accnos=groupnames.accnos.dat
+#if $shared_in:
-#end if
+,shared=shared_in.dat
-#if $fasta_in:
+#end if
-,fasta=fasta_in.dat
+#if $taxonomy_in:
-#end if
+,taxonomy=taxonomy_in.dat
-#if $name_in:
+#end if
-,name=name_in.dat
+#if $design_in:
-#end if
+,design=design_in.dat
-#if $list_in:
+#end if
-,list=list_in.dat
+#if $column_in:
-#end if
+,column=column_in.dat
-#if $shared_in:
+#end if
-,shared=shared_in.dat
+#if $phylip_in:
-#end if
+,phylip=phylip_in.dat
-#if $taxonomy_in:
+#end if
-,taxonomy=taxonomy_in.dat
+)'
-#end if
+| sed 's/ //g'  ## mothur trips over whitespace
-#if $design_in:
+| mothur
-,design=design_in.dat
+| tee mothur.out.log
-#end if
-)'
-| sed 's/ //g'  ## mothur trips over whitespace
-| mothur
-| tee mothur.out.log
 ]]></command>
 <inputs>
-<param name="group_in" type="data" format="mothur.groups,mothur.count_table" label="group or count_table file"/>
+<param name="group_in" type="data" format="mothur.groups,mothur.count_table" optional="true" label="group or count_table file"/>
+<param name="shared_in" type="data" format="mothur.shared" optional="true" label="shared - OTU Shared"/>
+<param name="design_in" type="data" format="tabular" optional="true" label="design - assign groups to new grouping"
+help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character) use make.design"/>
 <conditional name="groupnames">
 <param name="source" type="select" label="Select Group Names from">
 <option value="groups">A List of Group Names</option>
 <option value="accnos">A History Group Name Accnos Dataset</option>
 </param>
 </when>
 </conditional>
 <param name="fasta_in" type="data" format="fasta,mothur.align" optional="true" label="fasta - Fasta Sequences"/>
 <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
 <param name="list_in" type="data" format="mothur.list" optional="true" label="list - OTU List"/>
-<param name="shared_in" type="data" format="mothur.shared" optional="true" label="shared - OTU Shared"/>
 <param name="taxonomy_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/>
-<param name="design_in" type="data" format="tabular" optional="true" label="design - assign groups to new grouping" help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character) use make.design"/>
+<param name="phylip_in" type="data" format="mothur.lower.dist,mothur.square.dist" optional="true" label="phylip - Distance Matrix you would like to select distances from"
+help="must be a phylip-formatted distance matrix"/>
+<param name="column_in" type="data" format="mothur.pair.dist" optional="true" label="column - Distance Matrix you would like to select distances from"
+help="must be a column-formatted distance matrix"/>
 </inputs>
 <outputs>
 <expand macro="logfile-output"/>
 <data name="group_out" format="mothur.groups" from_work_dir="group_in*.pick.*" label="${tool.name} on ${on_string}: pick.groups">
 <filter>group_in.ext == "mothur.groups"</filter>
 <data name="taxonomy_out" format="mothur.seq.taxonomy" from_work_dir="taxonomy_in*.pick.*" label="${tool.name} on ${on_string}: pick.taxonomy">
 <filter>taxonomy_in</filter>
 </data>
 <data name="design_out" format="mothur.design" from_work_dir="design_in*.pick.*" label="${tool.name} on ${on_string}: pick.design">
 <filter>design_in</filter>
+</data>
+<data name="phylip_out" format_source="phylip_in" from_work_dir="phylip_in*.pick.*" label="${tool.name} on ${on_string}: pick.phylip">
+<filter>phylip_in</filter>
+</data>
+<data name="column_out" format="mothur.pair.dist" from_work_dir="column_in*.pick.*" label="${tool.name} on ${on_string}: pick.column">
+<filter>column_in</filter>
 </data>
 </outputs>
 <tests>
 <test><!-- test with group file -->
 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
 <output_collection name="sharedfiles" count="36">
 <element name="0.38" md5="3c78742e0a480ca3353f9b591fc9bf36" ftype="mothur.shared"/>
 </output_collection>
 <expand macro="logfile-test"/>
 </test>
+<test><!-- test with distance matrix -->
+<param name="group_in" value="amazon_withgroups.count_table" ftype="mothur.count_table"/>
+<param name="source" value="accnos"/>
+<param name="accnos" value="amazon.groupaccnos" ftype="mothur.accnos"/>
+<param name="column_in" value="amazon.pair.dist" ftype="mothur.pair.dist"/>
+<param name="phylip_in" value="amazon.dist" ftype="mothur.square.dist"/>
+<output name="column_out" ftype="mothur.pair.dist">
+<assert_contents>
+<expand macro="test-column-format"/>
+<has_text text="U68589"/>
+</assert_contents>
+</output>
+<output name="phylip_out" ftype="mothur.square.dist">
+<assert_contents>
+<expand macro="test-dist-format"/>
+<has_text text="U68589"/>
+</assert_contents>
+</output>
+<expand macro="logfile-test"/>
+</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
 .. _taxonomy: https://www.mothur.org/wiki/Taxonomy_outline
 .. _get.groups: https://www.mothur.org/wiki/Get.groups
-]]>
+]]></help>
-</help>
 <expand macro="citations"/>
 </tool>

Mercurial > repos > iuc > mothur_get_groups

comparison get.groups.xml @ 3:378f8103cf1b draft