Mercurial > repos > devteam > cufflinks
annotate cuff_macros.xml @ 9:a1ea9af8d5f4 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit a1517c9d22029095120643bbe2c8fa53754dd2b7
| author | devteam |
|---|---|
| date | Wed, 11 Nov 2015 12:34:49 -0500 |
| parents | 5346d5eea8b1 |
| children | 83bec71c5c9f |
| rev | line source |
|---|---|
| 7 | 1 <macros> |
| 2 <token name="@VERSION@">2.2.1</token> | |
| 3 <xml name="requirements"> | |
| 4 <requirements> | |
| 5 <requirement type="package" version="2.2.1">cufflinks</requirement> | |
| 6 <yield /> | |
| 7 </requirements> | |
| 8 </xml> | |
| 9 <xml name="stdio"> | |
| 10 <stdio> | |
| 11 <exit_code range="1:" /> | |
| 12 <exit_code range=":-1" /> | |
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9
a1ea9af8d5f4
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
7
diff
changeset
|
13 <regex match="Error" /> |
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a1ea9af8d5f4
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
7
diff
changeset
|
14 <regex match="Exception" /> |
| 7 | 15 </stdio> |
| 16 </xml> | |
| 17 <xml name="condition_inputs"> | |
| 18 <!-- DEFAULT : use BAM/SAM files --> | |
| 19 <conditional name="in_type"> | |
| 20 <param name="set_in_type" type="select" label="Input data type" | |
| 21 help="CuffNorm supports either CXB (from cuffquant) or SAM/BAM input files. Mixing is not supported. Default: SAM/BAM"> | |
| 22 <option value="BAM">SAM/BAM</option> | |
| 23 <option value="CXB">Cuffquant (CXB)</option> | |
| 24 <option value="CONDITION_LIST">List of single replicate conditions</option> | |
| 25 <option value="CONDITION_REPLICATE_LIST">List of multiple replicate conditions</option> | |
| 26 </param> | |
| 27 <when value="BAM"> | |
| 28 <repeat name="conditions" title="Condition" min="2"> | |
| 29 <param name="name" title="Condition name" type="text" label="Name"/> | |
| 30 <param name="samples" label="Replicates" type="data" format="sam,bam" multiple="true"/> | |
| 31 </repeat> | |
| 32 </when> | |
| 33 <when value="CXB"> | |
| 34 <repeat name="conditions" title="Condition" min="2"> | |
| 35 <param name="name" title="Condition name" type="text" label="Name"/> | |
| 36 <param name="samples" label="Replicates" type="data" format="cxb" multiple="true"/> | |
| 37 </repeat> | |
| 38 </when> | |
| 39 <when value="CONDITION_LIST"> | |
| 40 <param name="conditions" title="List of Conditions" type="data_collection" collection_type="list" /> | |
| 41 </when> | |
| 42 <when value="CONDITION_REPLICATE_LIST"> | |
| 43 <param name="conditions" title="List of Conditions" type="data_collection" collection_type="list:list" /> | |
| 44 </when> | |
| 45 </conditional> | |
| 46 </xml> | |
| 47 <token name="@CONDITION_SAMPLES@"> | |
| 48 #if $in_type.set_in_type in ['BAM', 'CXB'] | |
| 49 #for $condition in $in_type.conditions: | |
| 50 #set samples = ','.join( [ str( $sample ) for $sample in $condition.samples ] ) | |
| 51 $samples | |
| 52 #end for | |
| 53 #elif $in_type.set_in_type == 'CONDITION_LIST' | |
| 54 #for $sample in $in_type.conditions: | |
| 55 $sample | |
| 56 #end for | |
| 57 #elif $in_type.set_in_type == 'CONDITION_REPLICATE_LIST' | |
| 58 #for $condition_list in $in_type.conditions: | |
| 59 #set samples = ','.join( [ str( $sample ) for $sample in $condition_list ] ) | |
| 60 $samples | |
| 61 #end for | |
| 62 #end if | |
| 63 </token> | |
| 64 <token name="@CONDITION_LABELS@"> | |
| 65 #import re | |
| 66 #if $in_type.set_in_type in ['BAM', 'CXB'] | |
| 67 #set labels = '\'' + '\',\''.join( [ str( $condition.name ) for $condition in $in_type.conditions ] ) + '\'' | |
| 68 #elif $in_type.set_in_type in ['CONDITION_LIST', 'CONDITION_REPLICATE_LIST'] | |
| 69 #set labels = '\'' + '\',\''.join( map(lambda x: re.sub('[^\w\-_]', '_', x), $in_type.conditions.keys() ) ) + '\'' | |
| 70 #end if | |
| 71 --labels $labels | |
| 72 </token> | |
| 73 <xml name="cufflinks_gtf_inputs"> | |
| 74 <param format="gtf" name="inputs" type="data" label="GTF file(s) produced by Cufflinks" help="" multiple="true" /> | |
| 75 <repeat name="additional_inputs" title="Additional GTF Inputs (Lists)"> | |
| 76 <param format="gtf" name="additional_inputs" type="data_collection" label="GTF file(s) produced by Cufflinks" help="" /> | |
| 77 </repeat> | |
| 78 </xml> | |
| 79 <token name="@CUFFLINKS_GTF_INPUTS@"> | |
| 80 ## Inputs. | |
| 81 #for $input_file in $inputs: | |
| 82 "${input_file}" | |
| 83 #end for | |
| 84 #for $additional_input in $additional_inputs: | |
| 85 #for $input_file in $additional_input.additional_inputs: | |
| 86 "${input_file}" | |
| 87 #end for | |
| 88 #end for | |
| 89 </token> | |
| 90 <token name="@HAS_MULTIPLE_INPUTS@">getattr(inputs, "__len__", [].__len__)() >= 2</token> | |
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9
a1ea9af8d5f4
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
7
diff
changeset
|
91 </macros> |