Mercurial > repos > devteam > cufflinks
view cuff_macros.xml @ 11:e04dbae2abe0 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5
author | devteam |
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date | Sun, 19 Feb 2017 12:12:28 -0500 |
parents | 83bec71c5c9f |
children | d080005cffe1 |
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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="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" 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" 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" label="List of Conditions" type="data_collection" collection_type="list" /> </when> <when value="CONDITION_REPLICATE_LIST"> <param name="conditions" label="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>