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view cuff_macros.xml @ 0:baeea9c2ff0f draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
author | devteam |
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date | Mon, 09 Nov 2015 12:06:36 -0500 |
parents | |
children | 96c4d0e18546 |
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<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:" /> <exit_code range=":-1" /> <regex match="Error" /> <regex match="Exception" /> </stdio> </xml> <xml name="condition_inputs"> <!-- DEFAULT : use BAM/SAM files --> <conditional name="in_type"> <param name="set_in_type" type="select" label="Input data type" help="CuffNorm supports either CXB (from cuffquant) or SAM/BAM input files. Mixing is not supported. Default: SAM/BAM"> <option value="BAM">SAM/BAM</option> <option value="CXB">Cuffquant (CXB)</option> <option value="CONDITION_LIST">List of single replicate conditions</option> <option value="CONDITION_REPLICATE_LIST">List of multiple replicate conditions</option> </param> <when value="BAM"> <repeat name="conditions" title="Condition" min="2"> <param name="name" title="Condition name" type="text" label="Name"/> <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="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" /> </when> <when value="CONDITION_REPLICATE_LIST"> <param name="conditions" title="List of Conditions" type="data_collection" collection_type="list:list" /> </when> </conditional> </xml> <token name="@CONDITION_SAMPLES@"> #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 #end for #elif $in_type.set_in_type == 'CONDITION_LIST' #for $sample in $in_type.conditions: $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 #end for #end if </token> <token name="@CONDITION_LABELS@"> #import re #if $in_type.set_in_type in ['BAM', 'CXB'] #set labels = '\'' + '\',\''.join( [ str( $condition.name ) for $condition in $in_type.conditions ] ) + '\'' #elif $in_type.set_in_type in ['CONDITION_LIST', 'CONDITION_REPLICATE_LIST'] #set labels = '\'' + '\',\''.join( map(lambda x: re.sub('[^\w\-_]', '_', x), $in_type.conditions.keys() ) ) + '\'' #end if --labels $labels </token> <xml name="cufflinks_gtf_inputs"> <param format="gtf" name="inputs" type="data" label="GTF file(s) produced by Cufflinks" help="" multiple="true" /> <repeat name="additional_inputs" title="Additional GTF Inputs (Lists)"> <param format="gtf" name="additional_inputs" type="data_collection" label="GTF file(s) produced by Cufflinks" help="" /> </repeat> </xml> <token name="@CUFFLINKS_GTF_INPUTS@"> ## Inputs. #for $input_file in $inputs: "${input_file}" #end for #for $additional_input in $additional_inputs: #for $input_file in $additional_input.additional_inputs: "${input_file}" #end for #end for </token> <token name="@HAS_MULTIPLE_INPUTS@">getattr(inputs, "__len__", [].__len__)() >= 2</token> </macros>