Mercurial > repos > devteam > cuffdiff
view cuff_macros.xml @ 17:43221aef70e2 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 0e1d7660ab8ccb677b4f79207f5bc78097640f04"
author | iuc |
---|---|
date | Sat, 27 Nov 2021 09:58:11 +0000 |
parents | af3e173cad7f |
children | a85acc5199c7 |
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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="conditions_repeat" token_format=""> <repeat name="conditions" title="Condition" min="2"> <param name="name" label="Condition name" type="text"> <validator type="empty_field" message="You must provide a condition name" /> <validator type="expression" message="Commas are not allowed in condition names">value and "," not in value</validator> </param> <param name="samples" label="Replicates" type="data" format="@FORMAT@" multiple="true"/> </repeat> </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"> <expand macro="conditions_repeat" format="sam,bam" /> </when> <when value="CXB"> <expand macro="conditions_repeat" format="cxb" /> </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@"><![CDATA[ #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@"><![CDATA[ #import re #if $in_type.set_in_type in ['BAM', 'CXB'] #set labels = "','".join([str($condition.name) for $condition in $in_type.conditions]) #elif $in_type.set_in_type in ['CONDITION_LIST', 'CONDITION_REPLICATE_LIST'] #set labels = "','".join([str($condition).replace(',', '_') for $condition in $in_type.conditions.keys()]) #end if --labels '$labels' ]]></token> <xml name="cufflinks_gtf_inputs"> <param format="gtf" name="inputs" type="data" label="GTF file(s) produced by Cufflinks" help="" multiple="true" /> </xml> <token name="@CUFFLINKS_LINK_GTF_INPUTS@"><![CDATA[ ## Inputs. #for $i, $input_file in enumerate($inputs): ln -s '${input_file}' input_$i && #end for ]]></token> <token name="@CUFFLINKS_GTF_INPUTS@"><![CDATA[ ## Inputs. #for $i, $input_file in enumerate($inputs): 'input_$i' #end for ]]></token> <token name="@HAS_MULTIPLE_INPUTS@">getattr(inputs, "__len__", [].__len__)() >= 2</token> <xml name="citations"> <citations> <citation type="doi">10.1038/nbt.1621</citation> <yield/> </citations> </xml> </macros>