Mercurial > repos > devteam > cuffdiff
diff cuff_macros.xml @ 3:9ec1cc10742c draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
author | devteam |
---|---|
date | Tue, 07 Feb 2017 18:38:03 -0500 |
parents | 9ba750f285e3 |
children | e20b05db0839 |
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--- a/cuff_macros.xml Thu Oct 29 22:33:47 2015 -0400 +++ b/cuff_macros.xml Tue Feb 07 18:38:03 2017 -0500 @@ -1,11 +1,13 @@ <macros> <token name="@VERSION@">2.2.1</token> + <xml name="requirements"> <requirements> <requirement type="package" version="2.2.1">cufflinks</requirement> <yield /> </requirements> </xml> + <xml name="stdio"> <stdio> <exit_code range="1:" /> @@ -26,21 +28,21 @@ </param> <when value="BAM"> <repeat name="conditions" title="Condition" min="2"> - <param name="name" title="Condition name" type="text" label="Name"/> + <param name="name" label="Condition name" type="text"/> <param name="samples" label="Replicates" type="data" format="sam,bam" multiple="true"/> </repeat> </when> <when value="CXB"> <repeat name="conditions" title="Condition" min="2"> - <param name="name" title="Condition name" type="text" label="Name"/> + <param name="name" label="Condition name" type="text"/> <param name="samples" label="Replicates" type="data" format="cxb" multiple="true"/> </repeat> </when> <when value="CONDITION_LIST"> - <param name="conditions" title="List of Conditions" type="data_collection" collection_type="list" /> + <param name="conditions" label="List of Conditions" type="data_collection" collection_type="list" /> </when> <when value="CONDITION_REPLICATE_LIST"> - <param name="conditions" title="List of Conditions" type="data_collection" collection_type="list:list" /> + <param name="conditions" label="List of Conditions" type="data_collection" collection_type="list:list" /> </when> </conditional> </xml> @@ -48,16 +50,16 @@ #if $in_type.set_in_type in ['BAM', 'CXB'] #for $condition in $in_type.conditions: #set samples = ','.join( [ str( $sample ) for $sample in $condition.samples ] ) - $samples + '$samples' #end for #elif $in_type.set_in_type == 'CONDITION_LIST' #for $sample in $in_type.conditions: - $sample + '$sample' #end for #elif $in_type.set_in_type == 'CONDITION_REPLICATE_LIST' #for $condition_list in $in_type.conditions: #set samples = ','.join( [ str( $sample ) for $sample in $condition_list ] ) - $samples + '$samples' #end for #end if </token> @@ -79,11 +81,11 @@ <token name="@CUFFLINKS_GTF_INPUTS@"> ## Inputs. #for $input_file in $inputs: - "${input_file}" + '${input_file}' #end for #for $additional_input in $additional_inputs: #for $input_file in $additional_input.additional_inputs: - "${input_file}" + '${input_file}' #end for #end for </token>