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comparison cuff_macros.xml @ 5:93148c05136f draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffquant commit 80b06e80066b32ad53ed418628992f056444256f
author iuc
date Sat, 05 Oct 2024 11:16:30 +0000
parents 679d93c99757
children
comparison
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4:679d93c99757 5:93148c05136f
1 <macros> 1 <macros>
2 <token name="@VERSION@">2.2.1</token> 2 <token name="@TOOL_VERSION@">2.2.1</token>
3 <token name="@PROFILE@">23.1</token>
3 4
4 <xml name="requirements"> 5 <xml name="requirements">
5 <requirements> 6 <requirements>
6 <requirement type="package" version="2.2.1">cufflinks</requirement> 7 <requirement type="package" version="@TOOL_VERSION@">cufflinks</requirement>
7 <yield /> 8 <yield />
8 </requirements> 9 </requirements>
9 </xml> 10 </xml>
10 11
11 <xml name="condition_inputs"> 12 <xml name="conditions_repeat" token_format="">
12 <!-- DEFAULT : use BAM/SAM files --> 13 <repeat name="conditions" title="Condition" min="2">
13 <conditional name="in_type"> 14 <param name="name" label="Condition name" type="text">
14 <param name="set_in_type" type="select" label="Input data type" 15 <validator type="empty_field" message="You must provide a condition name" />
15 help="CuffNorm supports either CXB (from cuffquant) or SAM/BAM input files. Mixing is not supported. Default: SAM/BAM"> 16 <validator type="expression" message="Commas are not allowed in condition names">value and "," not in value</validator>
16 <option value="BAM">SAM/BAM</option> 17 </param>
17 <option value="CXB">Cuffquant (CXB)</option> 18 <param name="samples" label="Replicates" type="data" format="@FORMAT@" multiple="true"/>
18 <option value="CONDITION_LIST">List of single replicate conditions</option> 19 </repeat>
19 <option value="CONDITION_REPLICATE_LIST">List of multiple replicate conditions</option> 20 </xml>
20 </param>
21 <when value="BAM">
22 <repeat name="conditions" title="Condition" min="2">
23 <param name="name" label="Condition name" type="text"/>
24 <param name="samples" label="Replicates" type="data" format="sam,bam" multiple="true"/>
25 </repeat>
26 </when>
27 <when value="CXB">
28 <repeat name="conditions" title="Condition" min="2">
29 <param name="name" label="Condition name" type="text"/>
30 <param name="samples" label="Replicates" type="data" format="cxb" multiple="true"/>
31 </repeat>
32 </when>
33 <when value="CONDITION_LIST">
34 <param name="conditions" label="List of Conditions" type="data_collection" collection_type="list" />
35 </when>
36 <when value="CONDITION_REPLICATE_LIST">
37 <param name="conditions" label="List of Conditions" type="data_collection" collection_type="list:list" />
38 </when>
39 </conditional>
40 </xml>
41 <token name="@CONDITION_SAMPLES@">
42 #if $in_type.set_in_type in ['BAM', 'CXB']
43 #for $condition in $in_type.conditions:
44 #set samples = ','.join( [ str( $sample ) for $sample in $condition.samples ] )
45 '$samples'
46 #end for
47 #elif $in_type.set_in_type == 'CONDITION_LIST'
48 #for $sample in $in_type.conditions:
49 '$sample'
50 #end for
51 #elif $in_type.set_in_type == 'CONDITION_REPLICATE_LIST'
52 #for $condition_list in $in_type.conditions:
53 #set samples = ','.join( [ str( $sample ) for $sample in $condition_list ] )
54 '$samples'
55 #end for
56 #end if
57 </token>
58 <token name="@CONDITION_LABELS@">
59 #import re
60 #if $in_type.set_in_type in ['BAM', 'CXB']
61 #set labels = '\'' + '\',\''.join( [ str( $condition.name ) for $condition in $in_type.conditions ] ) + '\''
62 #elif $in_type.set_in_type in ['CONDITION_LIST', 'CONDITION_REPLICATE_LIST']
63 #set labels = '\'' + '\',\''.join( map(lambda x: re.sub('[^\w\-_]', '_', x), $in_type.conditions.keys() ) ) + '\''
64 #end if
65 --labels $labels
66 </token>
67 <xml name="cufflinks_gtf_inputs">
68 <param format="gtf" name="inputs" type="data" label="GTF file(s) produced by Cufflinks" help="" multiple="true" />
69 </xml>
70 <token name="@CUFFLINKS_LINK_GTF_INPUTS@"><![CDATA[
71 ## Inputs.
72 #for $i, $input_file in enumerate($inputs):
73 ln -s '${input_file}' input_$i &&
74 #end for
75 ]]></token>
76 <token name="@CUFFLINKS_GTF_INPUTS@">
77 ## Inputs.
78 #for $i, $input_file in enumerate($inputs):
79 'input_$i'
80 #end for
81 </token>
82 <token name="@HAS_MULTIPLE_INPUTS@">getattr(inputs, "__len__", [].__len__)() >= 2</token>
83 21
84 <xml name="citations"> 22 <xml name="condition_inputs">
85 <citations> 23 <!-- DEFAULT : use BAM/SAM files -->
86 <citation type="doi">10.1038/nbt.1621</citation> 24 <conditional name="in_type">
87 <yield/> 25 <param name="set_in_type" type="select" label="Input data type"
88 </citations> 26 help="CuffNorm supports either CXB (from cuffquant) or SAM/BAM input files. Mixing is not supported. Default: SAM/BAM">
89 </xml> 27 <option value="BAM">SAM/BAM</option>
28 <option value="CXB">Cuffquant (CXB)</option>
29 <option value="CONDITION_LIST">List of single replicate conditions</option>
30 <option value="CONDITION_REPLICATE_LIST">List of multiple replicate conditions</option>
31 </param>
32 <when value="BAM">
33 <expand macro="conditions_repeat" format="sam,bam" />
34 </when>
35 <when value="CXB">
36 <expand macro="conditions_repeat" format="cxb" />
37 </when>
38 <when value="CONDITION_LIST">
39 <param name="conditions" label="List of Conditions" type="data_collection" collection_type="list" />
40 </when>
41 <when value="CONDITION_REPLICATE_LIST">
42 <param name="conditions" label="List of Conditions" type="data_collection" collection_type="list:list" />
43 </when>
44 </conditional>
45 </xml>
46 <token name="@CONDITION_SAMPLES@"><![CDATA[
47 #if $in_type.set_in_type in ['BAM', 'CXB']
48 #for $condition in $in_type.conditions:
49 #set samples = ','.join([str($sample) for $sample in $condition.samples])
50 '$samples'
51 #end for
52 #elif $in_type.set_in_type == 'CONDITION_LIST'
53 #for $sample in $in_type.conditions:
54 '$sample'
55 #end for
56 #elif $in_type.set_in_type == 'CONDITION_REPLICATE_LIST'
57 #for $condition_list in $in_type.conditions:
58 #set samples = ','.join([str($sample) for $sample in $condition_list])
59 '$samples'
60 #end for
61 #end if
62 ]]></token>
63 <token name="@CONDITION_LABELS@"><![CDATA[
64 #import re
65 #if $in_type.set_in_type in ['BAM', 'CXB']
66 #set labels = "','".join([str($condition.name) for $condition in $in_type.conditions])
67 #elif $in_type.set_in_type in ['CONDITION_LIST', 'CONDITION_REPLICATE_LIST']
68 #set labels = "','".join([str($condition).replace(',', '_') for $condition in $in_type.conditions.keys()])
69 #end if
70 --labels '$labels'
71 ]]></token>
72 <xml name="cufflinks_gtf_inputs">
73 <param format="gtf" name="inputs" type="data" label="GTF file(s) produced by Cufflinks" help="" multiple="true" />
74 </xml>
75 <token name="@CUFFLINKS_LINK_GTF_INPUTS@"><![CDATA[
76 ## Inputs.
77 #for $i, $input_file in enumerate($inputs):
78 ln -s '${input_file}' input_$i &&
79 #end for
80 ]]></token>
81 <token name="@CUFFLINKS_GTF_INPUTS@"><![CDATA[
82 ## Inputs.
83 #for $i, $input_file in enumerate($inputs):
84 'input_$i'
85 #end for
86 ]]></token>
87 <token name="@HAS_MULTIPLE_INPUTS@">getattr(inputs, "__len__", [].__len__)() >= 2</token>
88
89 <xml name="citations">
90 <citations>
91 <citation type="doi">10.1038/nbt.1621</citation>
92 <yield/>
93 </citations>
94 </xml>
90 95
91 </macros> 96 </macros>