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comparison cooler_csort_tabix.xml @ 1:d56db0e1555d draft

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planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit f7ba0eeedb7768690962c0538df0507110605f43
author lldelisle
date Thu, 01 Dec 2022 11:21:20 +0000
parents 36d7d522f13e
children
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0:36d7d522f13e 1:d56db0e1555d
1 <tool id="cooler_csort_tabix" name="cooler csort with tabix" version="@VERSION@+galaxy0" profile="18.01"> 1 <tool id="cooler_csort_tabix" name="cooler csort with tabix" version="@VERSION@+galaxy1" profile="22.05">
2 <description> Sort and index a contact list.</description> 2 <description> Sort and index a contact list.</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <expand macro="stdio" /> 7 <expand macro="stdio" />
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 cooler csort -i tabix -c1 $c1 -c2 $c2 -p1 $p1 -p2 $p2 -o '$output' '$input' 9 cooler csort -i tabix
10 #if str($format_sel.format) == "juicer_medium":
11 -c1 3 -c2 7 -p1 4 -p2 8
12 #else:
13 -c1 $format_sel.c1 -c2 $format_sel.c2 -p1 $format_sel.p1 -p2 $format_sel.p2
14 #end if
15 -o '$output' '$input'
10 #if str($size_source.size_source_selector) == 'history': 16 #if str($size_source.size_source_selector) == 'history':
11 '$size_source.chromosomeSize' 17 '$size_source.chromosomeSize'
12 #else: 18 #else:
13 '$size_source.fasta_cached.fields.path'.fai 19 '$size_source.fasta_cached.fields.path'.fai
14 #end if 20 #end if
15 ]]> 21 ]]>
16 </command> 22 </command>
17 <inputs> 23 <inputs>
18 <param name="input" multiple="false" type="data" format="tabular" label="Select a file with the coordinates of the pairs (minimum 4 columns with chromosome and position for each mate)."/> 24 <param name="input" multiple="false" type="data" format="tabular" label="Select a file with the coordinates of the pairs (minimum 4 columns with chromosome and position for each mate)."/>
19 <param name="c1" type="integer" value="1" label="field number in the input file (starting from 1) of the chromosome of mate 1."> 25 <conditional name="format_sel">
20 <validator type="in_range" min="1" /> 26 <param name="format" type="select" label="Format of your input file">
21 </param> 27 <option value="juicer_medium">Juicer Medium Format</option>
22 <param name="p1" type="integer" value="2" label="field number in the input file (starting from 1) of the position of mate 1."> 28 <option value="other">Other</option>
23 <validator type="in_range" min="1" /> 29 </param>
24 </param> 30 <when value="juicer_medium"/>
25 <param name="c2" type="integer" value="3" label="field number in the input file (starting from 1) of the chromosome of mate 2."> 31 <when value="other">
26 <validator type="in_range" min="1" /> 32 <param name="c1" type="integer" value="1" label="field number in the input file (starting from 1) of the chromosome of mate 1.">
27 </param> 33 <validator type="in_range" min="1" />
28 <param name="p2" type="integer" value="4" label="field number in the input file (starting from 1) of the position of mate 2."> 34 </param>
29 <validator type="in_range" min="1" /> 35 <param name="p1" type="integer" value="2" label="field number in the input file (starting from 1) of the position of mate 1.">
30 </param> 36 <validator type="in_range" min="1" />
37 </param>
38 <param name="c2" type="integer" value="3" label="field number in the input file (starting from 1) of the chromosome of mate 2.">
39 <validator type="in_range" min="1" />
40 </param>
41 <param name="p2" type="integer" value="4" label="field number in the input file (starting from 1) of the position of mate 2.">
42 <validator type="in_range" min="1" />
43 </param>
44 </when>
45 </conditional>
31 <expand macro="size_macro" /> 46 <expand macro="size_macro" />
32 </inputs> 47 </inputs>
33 48
34 <outputs> 49 <outputs>
35 <data format="tabix" name="output" label="sorted and indexed contact list of $input.name"/> 50 <data format="interval_tabix.gz" name="output" label="sorted and indexed contact list of $input.name">
51 <actions>
52 <conditional name="format_sel.format">
53 <when value="juicer_medium">
54 <action type="format" default="juicer_medium_tabix.gz" />
55 </when>
56 <when value="other">
57 <action type="metadata" name="chromCol" default="$format_sel.c1"/>
58 <action type="metadata" name="startCol" default="$format_sel.p1"/>
59 <action type="metadata" name="endCol" default="$format_sel.p1"/>
60 </when>
61 </conditional>
62 </actions>
63 </data>
36 </outputs> 64 </outputs>
37 65
38 <tests> 66 <tests>
39 <test> 67 <test>
40 <param name="input" value="input.validPairs.txt"/> 68 <param name="input" value="input.validPairs.txt"/>
41 <conditional name="size_source"> 69 <conditional name="size_source">
42 <param name="size_source_selector" value="history"/> 70 <param name="size_source_selector" value="history"/>
43 <param name="chromosomeSize" value="chr19.size"/> 71 <param name="chromosomeSize" value="chr19.size"/>
44 </conditional> 72 </conditional>
45 <param name="c1" value="3"/> 73 <conditional name="format_sel">
46 <param name="p1" value="4"/> 74 <param name="format" value="juicer_medium"/>
47 <param name="c2" value="7"/> 75 </conditional>
48 <param name="p2" value="8"/> 76 <output name="output" file="input.validPairs.tabix" decompress="true">
49 <output name="output" file="input.validPairs.tabix" decompress="true"/> 77 <metadata name="chromCol" value="3" />
78 <metadata name="startCol" value="4" />
79 <metadata name="endCol" value="4" />
80 </output>
81 </test>
82 <test>
83 <param name="input" value="input.validPairs.txt"/>
84 <conditional name="size_source">
85 <param name="size_source_selector" value="history"/>
86 <param name="chromosomeSize" value="chr19.size"/>
87 </conditional>
88 <conditional name="format_sel">
89 <param name="format" value="other"/>
90 <param name="c1" value="3"/>
91 <param name="p1" value="4"/>
92 <param name="c2" value="7"/>
93 <param name="p2" value="8"/>
94 </conditional>
95 <output name="output" file="input.validPairs.tabix" decompress="true">
96 <metadata name="chromCol" value="3" />
97 <metadata name="startCol" value="4" />
98 <metadata name="endCol" value="4" />
99 </output>
50 </test> 100 </test>
51 </tests> 101 </tests>
52 102
53 <help> 103 <help>
54 **cooler csort** 104 **cooler csort**