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comparison cooler_cload_tabix.xml @ 1:3ff6eeca667e 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 11:21:36 +0000
parents 8745321ccc3e
children
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0:8745321ccc3e 1:3ff6eeca667e
1 <tool id="cooler_cload_tabix" name="cooler_cload_tabix" version="@VERSION@+galaxy0" profile="18.01"> 1 <tool id="cooler_cload_tabix" name="cooler_cload_tabix" version="@VERSION@+galaxy1" profile="22.05">
2 <description> Create a cool file from a tabix-indexed contact file and a list of genomic bins.</description> 2 <description> Create a cool file from a tabix-indexed contact file and a list of genomic bins.</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 ##set up input files 9 ##set up input files
10 ln -s '$input_pairs' pairs.tabix && 10 ln -s '$format_sel.input_pairs' pairs.tabix &&
11 #if str( $input_pairs.metadata.tabix_index ) != "None": 11 ln -s '$format_sel.input_pairs.metadata.tabix_index' pairs.tabix.tbi &&
12 ln -s '$input_pairs.metadata.tabix_index' pairs.tabix.tbi && 12 cooler cload tabix --assembly '$assembly'
13 #if $format_sel.format == "juicer_medium":
14 -c2 7 -p2 8
13 #else: 15 #else:
14 tabix -s $pairs_advanced.c1 -b $pairs_advanced.p1 -e $pairs_advanced.p1 pairs.tabix && 16 -c2 $format_sel.c2 -p2 $format_sel.p2
15 #end if 17 #end if
16 cooler cload tabix --assembly '$assembly' -c2 $c2 -p2 $p2 '$input_bed' pairs.tabix '$output' 18 '$input_bed' pairs.tabix '$output'
17 ]]> 19 ]]>
18 </command> 20 </command>
19 <inputs> 21 <inputs>
20 <param name="input_pairs" multiple="false" type="data" format="bgzip,tabix" label="Select the output of csort_tabix."/> 22 <conditional name="format_sel">
21 <section name="pairs_advanced" title="If your input is not already indexed" expanded="False"> 23 <param name="format" type="select" label="Format of your input file">
22 <param name="c1" type="integer" value="1" label="field number in the input file (starting from 1) of the chromosome of mate 1."> 24 <option value="juicer_medium">Juicer Medium Format</option>
23 <validator type="in_range" min="1" /> 25 <option value="other">Other</option>
24 </param> 26 </param>
25 <param name="p1" type="integer" value="2" label="field number in the input file (starting from 1) of the position of mate 1."> 27 <when value="juicer_medium">
26 <validator type="in_range" min="1" /> 28 <param name="input_pairs" multiple="false" type="data" format="juicer_medium_tabix.gz" label="Select the output of csort_tabix."/>
27 </param> 29 </when>
28 </section> 30 <when value="other">
29 <param name="c2" type="integer" value="3" label="field number in the input file (starting from 1) of the chromosome of mate 2 (same as in csort)."> 31 <param name="input_pairs" multiple="false" type="data" format="interval_tabix.gz" label="Select the output of csort_tabix."/>
30 <validator type="in_range" min="1" /> 32 <param name="c2" type="integer" value="3" label="field number in the input file (starting from 1) of the chromosome of mate 2 (same as in csort).">
31 </param> 33 <validator type="in_range" min="1" />
32 <param name="p2" type="integer" value="4" label="field number in the input file (starting from 1) of the position of mate 2 (same as in csort)."> 34 </param>
33 <validator type="in_range" min="1" /> 35 <param name="p2" type="integer" value="4" label="field number in the input file (starting from 1) of the position of mate 2 (same as in csort).">
34 </param> 36 <validator type="in_range" min="1" />
37 </param>
38 </when>
39 </conditional>
35 <param name="assembly" type="text" label="name of genome assembly"/> 40 <param name="assembly" type="text" label="name of genome assembly"/>
36 <param name="input_bed" multiple="false" type="data" format="bed" label="Select the output of makebins."/> 41 <param name="input_bed" multiple="false" type="data" format="bed" label="Select the output of makebins."/>
37 </inputs> 42 </inputs>
38 43
39 <outputs> 44 <outputs>
40 <data format="cool" name="output" label="cool file from $input_pairs.name and $input_bed.name"/> 45 <data format="cool" name="output" label="cool file from $format_sel.input_pairs.name and $input_bed.name"/>
41 </outputs> 46 </outputs>
42 47
43 <tests> 48 <tests>
44 <!-- For the moment I cannot test this tool --> 49 <test>
45 <!-- <test> 50 <conditional name="format_sel">
46 <param name="input_pairs" value="input.validPairs.tabix" ftype="bgzip"/> 51 <param name="format" value="juicer_medium"/>
52 <param name="input_pairs" value="input.validPairs.tabix" ftype="juicer_medium_tabix.gz"/>
53 </conditional>
47 <param name="input_bed" value="chr19.1M.bins"/> 54 <param name="input_bed" value="chr19.1M.bins"/>
48 <param name="assembly" value="chr19"/> 55 <param name="assembly" value="chr19"/>
49 <section name="pairs_advanced">
50 <param name="c1" value="3"/>
51 <param name="p1" value="4"/>
52 </section>
53 <param name="c2" value="7"/>
54 <param name="p2" value="8"/>
55 <output name="output" file="input.cool" compare="sim_size"/> 56 <output name="output" file="input.cool" compare="sim_size"/>
56 </test> --> 57 </test>
58 <test>
59 <conditional name="format_sel">
60 <param name="format" value="other"/>
61 <param name="input_pairs" value="input.validPairs.tabix" ftype="juicer_medium_tabix.gz"/>
62 <param name="c2" value="7"/>
63 <param name="p2" value="8"/>
64 </conditional>
65 <param name="input_bed" value="chr19.1M.bins"/>
66 <param name="assembly" value="chr19"/>
67 <output name="output" file="input.cool" compare="sim_size"/>
68 </test>
57 </tests> 69 </tests>
58 70
59 <help> 71 <help>
60 **cooler cload** 72 **cooler cload**
61 tool developped by mirnylab 73 tool developped by mirnylab