Mercurial > repos > devteam > cuffdiff
annotate cuff_macros.xml @ 13:f1b92120dfaa 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 18:39:02 -0500 |
| parents | 5ce5197de50c |
| children | d3ae7d9c2202 |
| rev | line source |
|---|---|
| 7 | 1 <macros> |
| 2 <token name="@VERSION@">2.2.1</token> | |
|
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f1b92120dfaa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents:
11
diff
changeset
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3 |
| 7 | 4 <xml name="requirements"> |
| 5 <requirements> | |
| 6 <requirement type="package" version="2.2.1">cufflinks</requirement> | |
| 7 <yield /> | |
| 8 </requirements> | |
| 9 </xml> | |
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f1b92120dfaa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents:
11
diff
changeset
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10 |
| 7 | 11 <xml name="stdio"> |
| 12 <stdio> | |
| 13 <exit_code range="1:" /> | |
| 14 <exit_code range=":-1" /> | |
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5ce5197de50c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 220e70acb66016873732b193b3ac20ae48083f0b-dirty
devteam
parents:
7
diff
changeset
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15 <regex match="Error" /> |
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5ce5197de50c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 220e70acb66016873732b193b3ac20ae48083f0b-dirty
devteam
parents:
7
diff
changeset
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16 <regex match="Exception" /> |
| 7 | 17 </stdio> |
| 18 </xml> | |
| 19 <xml name="condition_inputs"> | |
| 20 <!-- DEFAULT : use BAM/SAM files --> | |
| 21 <conditional name="in_type"> | |
| 22 <param name="set_in_type" type="select" label="Input data type" | |
| 23 help="CuffNorm supports either CXB (from cuffquant) or SAM/BAM input files. Mixing is not supported. Default: SAM/BAM"> | |
| 24 <option value="BAM">SAM/BAM</option> | |
| 25 <option value="CXB">Cuffquant (CXB)</option> | |
| 26 <option value="CONDITION_LIST">List of single replicate conditions</option> | |
| 27 <option value="CONDITION_REPLICATE_LIST">List of multiple replicate conditions</option> | |
| 28 </param> | |
| 29 <when value="BAM"> | |
| 30 <repeat name="conditions" title="Condition" min="2"> | |
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13
f1b92120dfaa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents:
11
diff
changeset
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31 <param name="name" label="Condition name" type="text"/> |
| 7 | 32 <param name="samples" label="Replicates" type="data" format="sam,bam" multiple="true"/> |
| 33 </repeat> | |
| 34 </when> | |
| 35 <when value="CXB"> | |
| 36 <repeat name="conditions" title="Condition" min="2"> | |
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13
f1b92120dfaa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents:
11
diff
changeset
|
37 <param name="name" label="Condition name" type="text"/> |
| 7 | 38 <param name="samples" label="Replicates" type="data" format="cxb" multiple="true"/> |
| 39 </repeat> | |
| 40 </when> | |
| 41 <when value="CONDITION_LIST"> | |
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13
f1b92120dfaa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents:
11
diff
changeset
|
42 <param name="conditions" label="List of Conditions" type="data_collection" collection_type="list" /> |
| 7 | 43 </when> |
| 44 <when value="CONDITION_REPLICATE_LIST"> | |
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13
f1b92120dfaa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents:
11
diff
changeset
|
45 <param name="conditions" label="List of Conditions" type="data_collection" collection_type="list:list" /> |
| 7 | 46 </when> |
| 47 </conditional> | |
| 48 </xml> | |
| 49 <token name="@CONDITION_SAMPLES@"> | |
| 50 #if $in_type.set_in_type in ['BAM', 'CXB'] | |
| 51 #for $condition in $in_type.conditions: | |
| 52 #set samples = ','.join( [ str( $sample ) for $sample in $condition.samples ] ) | |
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13
f1b92120dfaa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents:
11
diff
changeset
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53 '$samples' |
| 7 | 54 #end for |
| 55 #elif $in_type.set_in_type == 'CONDITION_LIST' | |
| 56 #for $sample in $in_type.conditions: | |
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13
f1b92120dfaa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents:
11
diff
changeset
|
57 '$sample' |
| 7 | 58 #end for |
| 59 #elif $in_type.set_in_type == 'CONDITION_REPLICATE_LIST' | |
| 60 #for $condition_list in $in_type.conditions: | |
| 61 #set samples = ','.join( [ str( $sample ) for $sample in $condition_list ] ) | |
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13
f1b92120dfaa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents:
11
diff
changeset
|
62 '$samples' |
| 7 | 63 #end for |
| 64 #end if | |
| 65 </token> | |
| 66 <token name="@CONDITION_LABELS@"> | |
| 67 #import re | |
| 68 #if $in_type.set_in_type in ['BAM', 'CXB'] | |
| 69 #set labels = '\'' + '\',\''.join( [ str( $condition.name ) for $condition in $in_type.conditions ] ) + '\'' | |
| 70 #elif $in_type.set_in_type in ['CONDITION_LIST', 'CONDITION_REPLICATE_LIST'] | |
| 71 #set labels = '\'' + '\',\''.join( map(lambda x: re.sub('[^\w\-_]', '_', x), $in_type.conditions.keys() ) ) + '\'' | |
| 72 #end if | |
| 73 --labels $labels | |
| 74 </token> | |
| 75 <xml name="cufflinks_gtf_inputs"> | |
| 76 <param format="gtf" name="inputs" type="data" label="GTF file(s) produced by Cufflinks" help="" multiple="true" /> | |
| 77 <repeat name="additional_inputs" title="Additional GTF Inputs (Lists)"> | |
| 78 <param format="gtf" name="additional_inputs" type="data_collection" label="GTF file(s) produced by Cufflinks" help="" /> | |
| 79 </repeat> | |
| 80 </xml> | |
| 81 <token name="@CUFFLINKS_GTF_INPUTS@"> | |
| 82 ## Inputs. | |
| 83 #for $input_file in $inputs: | |
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13
f1b92120dfaa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents:
11
diff
changeset
|
84 '${input_file}' |
| 7 | 85 #end for |
| 86 #for $additional_input in $additional_inputs: | |
| 87 #for $input_file in $additional_input.additional_inputs: | |
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13
f1b92120dfaa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents:
11
diff
changeset
|
88 '${input_file}' |
| 7 | 89 #end for |
| 90 #end for | |
| 91 </token> | |
| 92 <token name="@HAS_MULTIPLE_INPUTS@">getattr(inputs, "__len__", [].__len__)() >= 2</token> | |
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11
5ce5197de50c
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 220e70acb66016873732b193b3ac20ae48083f0b-dirty
devteam
parents:
7
diff
changeset
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93 </macros> |