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comparison pretext_map.xml @ 0:f59b273119f7 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
author iuc
date Wed, 05 May 2021 15:08:17 +0000
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children 9781c90fb254
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-1:000000000000 0:f59b273119f7
1 <tool id="pretext_map" name="PretextMap" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
2 <macros>
3 <token name="@TOOL_VERSION@">0.1.5</token>
4 <token name="@VERSION_SUFFIX@">0</token>
5 </macros>
6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">pretextmap</requirement>
8 <requirement type="package" version="1.12">samtools</requirement>
9 </requirements>
10 <version_command>PretextMap --version</version_command>
11 <command detect_errors="exit_code"><![CDATA[
12 #if $input.is_of_type("bam"):
13 samtools view -h '${input}' |
14 #else
15 cat '${input}' |
16 #end if
17 PretextMap
18 #if $sorting.sortby == "length":
19 --sortby length
20 --sortorder $sorting.sortorder
21 #elif $sorting.sortby == "name":
22 --sortby name
23 --sortorder $sorting.sortorder
24 #end if
25 #if $map_qual:
26 --mapq $map_qual
27 #end if
28 #if $filter.filter_type == "in":
29 --filterInclude '$filter.filter_list'
30 #elif $filter.filter_type == "out":
31 --filterExclude '$filter.filter_list'
32 #end if
33 -o output.pretext
34 ]]></command>
35 <inputs>
36 <param name="input" type="data" format="sam,bam" label="Input dataset in SAM or BAM format"/>
37 <conditional name="sorting">
38 <param argument="--sortby" type="select" label="Sort by">
39 <option value="nosort" selected="true">Don't sort</option>
40 <option value="length">Length</option>
41 <option value="name">Name</option>
42 </param>
43 <when value="nosort"/>
44 <when value="length">
45 <param argument="--sortorder" type="select" label="Sort order: ">
46 <option value="ascend">Ascending</option>
47 <option value="decend">Decending</option>
48 </param>
49 </when>
50 <when value="name">
51 <param argument="--sortorder" type="select" label="Sort order: ">
52 <option value="ascend">Ascending</option>
53 <option value="descend">Decending</option>
54 </param>
55 </when>
56 </conditional>
57 <param name="map_qual" type="integer" label="Minimum mapping quality:" min="0" optional="true"/>
58 <conditional name="filter">
59 <param name="filter_type" type="select" label="How to filter: ">
60 <option value="" selected="true">No filter</option>
61 <option value="in">Filter to include only specified sequence names</option>
62 <option value="out">Filter to exclude specified sequence names</option>
63 </param>
64 <when value=""/>
65 <when value="in">
66 <param name="filter_list" type="text" label="Filter list" help="Comma separated list of sequence names to use as a filter" value="seq_1, seq_2">
67 <sanitizer>
68 <valid initial="string.ascii_letters,string.digits">
69 <add value="_"/>
70 </valid>
71 </sanitizer>
72 </param>
73 </when>
74 <when value="out">
75 <param name="filter_list" type="text" label="Filter list" help="Comma separated list of sequence names to use as a filter" value="seq_1, seq_2">
76 <sanitizer>
77 <valid initial="string.ascii_letters,string.digits">
78 <add value="_"/>
79 </valid>
80 </sanitizer>
81 </param>
82 </when>
83 </conditional>
84 </inputs>
85 <outputs>
86 <data format="pretext" name="pretext_map_out" from_work_dir="output.pretext" label="${tool.name} on ${on_string}"/>
87 </outputs>
88 <tests>
89 <test>
90 <param name="input" ftype="bam" value="test.bam"/>
91 <conditional name="sorting">
92 <param name="sortby" value="length"/>
93 <param name="sortorder" value="ascend"/>
94 </conditional>
95 <conditional name="filter">
96 <param name="filter_type" value="in"/>
97 <param name="filter_list" value="ref"/>
98 </conditional>
99 <param name="map_qual" value="10"/>
100 <output name="pretext_map_out" file="output_1.pretext"/>
101 </test>
102 <test>
103 <param name="input" ftype="sam" value="test.sam"/>
104 <conditional name="sorting">
105 <param name="sortby" value="name"/>
106 <param name="sortorder" value="descend"/>
107 </conditional>
108 <conditional name="filter">
109 <param name="filter_type" value="out"/>
110 <param name="filter_list" value="chrM, chr8, chr9"/>
111 </conditional>
112 <output name="pretext_map_out" file="output_2.pretext"/>
113 </test>
114 </tests>
115 <help><![CDATA[
116
117 **What is does**
118
119 The Paired REad TEXTure Mapper converts aligned read pairs into genome contact maps.
120 Pretext has no special requirement on the alignment files
121 process your alignments however you want before feeding to PretextMap.
122
123 ]]></help>
124 <citations>
125 <citation type="bibtex">
126 @misc{Harry_et_al,
127 Author={Harry, E},
128 title={Paired REad TEXTure Snapshot: Command line image generator for Pretext contact maps.},
129 url = {https://github.com/wtsi-hpag/PretextSnapshot},}
130 </citation>
131 </citations>
132 </tool>