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comparison cuff_macros.xml @ 12:1707a530e598 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffmerge commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
author devteam
date Tue, 07 Feb 2017 18:39:42 -0500
parents 8160c8ea4eb9
children cf747d1bd79a
comparison
equal deleted inserted replaced
11:8160c8ea4eb9 12:1707a530e598
1 <macros> 1 <macros>
2 <token name="@VERSION@">2.2.1</token> 2 <token name="@VERSION@">2.2.1</token>
3
3 <xml name="requirements"> 4 <xml name="requirements">
4 <requirements> 5 <requirements>
5 <requirement type="package" version="2.2.1">cufflinks</requirement> 6 <requirement type="package" version="2.2.1">cufflinks</requirement>
6 <yield /> 7 <yield />
7 </requirements> 8 </requirements>
8 </xml> 9 </xml>
10
9 <xml name="stdio"> 11 <xml name="stdio">
10 <stdio> 12 <stdio>
11 <exit_code range="1:" /> 13 <exit_code range="1:" />
12 <exit_code range=":-1" /> 14 <exit_code range=":-1" />
13 <regex match="Error" /> 15 <regex match="Error" />
24 <option value="CONDITION_LIST">List of single replicate conditions</option> 26 <option value="CONDITION_LIST">List of single replicate conditions</option>
25 <option value="CONDITION_REPLICATE_LIST">List of multiple replicate conditions</option> 27 <option value="CONDITION_REPLICATE_LIST">List of multiple replicate conditions</option>
26 </param> 28 </param>
27 <when value="BAM"> 29 <when value="BAM">
28 <repeat name="conditions" title="Condition" min="2"> 30 <repeat name="conditions" title="Condition" min="2">
29 <param name="name" title="Condition name" type="text" label="Name"/> 31 <param name="name" label="Condition name" type="text"/>
30 <param name="samples" label="Replicates" type="data" format="sam,bam" multiple="true"/> 32 <param name="samples" label="Replicates" type="data" format="sam,bam" multiple="true"/>
31 </repeat> 33 </repeat>
32 </when> 34 </when>
33 <when value="CXB"> 35 <when value="CXB">
34 <repeat name="conditions" title="Condition" min="2"> 36 <repeat name="conditions" title="Condition" min="2">
35 <param name="name" title="Condition name" type="text" label="Name"/> 37 <param name="name" label="Condition name" type="text"/>
36 <param name="samples" label="Replicates" type="data" format="cxb" multiple="true"/> 38 <param name="samples" label="Replicates" type="data" format="cxb" multiple="true"/>
37 </repeat> 39 </repeat>
38 </when> 40 </when>
39 <when value="CONDITION_LIST"> 41 <when value="CONDITION_LIST">
40 <param name="conditions" title="List of Conditions" type="data_collection" collection_type="list" /> 42 <param name="conditions" label="List of Conditions" type="data_collection" collection_type="list" />
41 </when> 43 </when>
42 <when value="CONDITION_REPLICATE_LIST"> 44 <when value="CONDITION_REPLICATE_LIST">
43 <param name="conditions" title="List of Conditions" type="data_collection" collection_type="list:list" /> 45 <param name="conditions" label="List of Conditions" type="data_collection" collection_type="list:list" />
44 </when> 46 </when>
45 </conditional> 47 </conditional>
46 </xml> 48 </xml>
47 <token name="@CONDITION_SAMPLES@"> 49 <token name="@CONDITION_SAMPLES@">
48 #if $in_type.set_in_type in ['BAM', 'CXB'] 50 #if $in_type.set_in_type in ['BAM', 'CXB']
49 #for $condition in $in_type.conditions: 51 #for $condition in $in_type.conditions:
50 #set samples = ','.join( [ str( $sample ) for $sample in $condition.samples ] ) 52 #set samples = ','.join( [ str( $sample ) for $sample in $condition.samples ] )
51 $samples 53 '$samples'
52 #end for 54 #end for
53 #elif $in_type.set_in_type == 'CONDITION_LIST' 55 #elif $in_type.set_in_type == 'CONDITION_LIST'
54 #for $sample in $in_type.conditions: 56 #for $sample in $in_type.conditions:
55 $sample 57 '$sample'
56 #end for 58 #end for
57 #elif $in_type.set_in_type == 'CONDITION_REPLICATE_LIST' 59 #elif $in_type.set_in_type == 'CONDITION_REPLICATE_LIST'
58 #for $condition_list in $in_type.conditions: 60 #for $condition_list in $in_type.conditions:
59 #set samples = ','.join( [ str( $sample ) for $sample in $condition_list ] ) 61 #set samples = ','.join( [ str( $sample ) for $sample in $condition_list ] )
60 $samples 62 '$samples'
61 #end for 63 #end for
62 #end if 64 #end if
63 </token> 65 </token>
64 <token name="@CONDITION_LABELS@"> 66 <token name="@CONDITION_LABELS@">
65 #import re 67 #import re
77 </repeat> 79 </repeat>
78 </xml> 80 </xml>
79 <token name="@CUFFLINKS_GTF_INPUTS@"> 81 <token name="@CUFFLINKS_GTF_INPUTS@">
80 ## Inputs. 82 ## Inputs.
81 #for $input_file in $inputs: 83 #for $input_file in $inputs:
82 "${input_file}" 84 '${input_file}'
83 #end for 85 #end for
84 #for $additional_input in $additional_inputs: 86 #for $additional_input in $additional_inputs:
85 #for $input_file in $additional_input.additional_inputs: 87 #for $input_file in $additional_input.additional_inputs:
86 "${input_file}" 88 '${input_file}'
87 #end for 89 #end for
88 #end for 90 #end for
89 </token> 91 </token>
90 <token name="@HAS_MULTIPLE_INPUTS@">getattr(inputs, "__len__", [].__len__)() >= 2</token> 92 <token name="@HAS_MULTIPLE_INPUTS@">getattr(inputs, "__len__", [].__len__)() >= 2</token>
91 </macros> 93 </macros>