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comparison rcorrector.xml @ 1:b84843d7a157 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit 65ada0f9589f3ffebad1db6636ccb50d58082606"
author iuc
date Thu, 26 Dec 2019 10:21:32 +0000
parents ec100df3085c
children 975a2bc42c0a
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0:ec100df3085c 1:b84843d7a157
1 <tool id="rcorrector" name="RNA-seq Rcorrector" version="1.0.3"> 1 <tool id="rcorrector" name="RNA-seq Rcorrector" version="1.0.3+galaxy1">
2 <description>a kmer-based error correction method for RNA-seq data</description> 2 <description>a kmer-based error correction method for RNA-seq data</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.0.3">rcorrector</requirement> 4 <requirement type="package" version="1.0.3">rcorrector</requirement>
5 <requirement type="package" version="3.7">python</requirement>
5 </requirements> 6 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
7 #if $library.lib == "single": 8 #if $library.lib == "single":
8 ln -s '$library.input1' input_1.fq && 9 ln -s '$library.input1' input_1.fq &&
9 #end if 10 #end if
15 -s input_1.fq 16 -s input_1.fq
16 #end if 17 #end if
17 #if $library.lib == "paired": 18 #if $library.lib == "paired":
18 -1 input_1.fq -2 input_2.fq 19 -1 input_1.fq -2 input_2.fq
19 #end if 20 #end if
20 -k '$advanced.kmers' -t \${GALAXY_SLOTS:-4} -maxcorK '$advanced.maxcorK' -wk '$advanced.wk' -ek '$advanced.ek' -od output_file_directory 21 -k '$advanced.kmers' -t \${GALAXY_SLOTS:-4} -maxcorK '$advanced.maxcorK' -wk '$advanced.wk' -ek '$advanced.ek' -od output_file_directory
21 22
22 #if $library.lib == "paired": 23 #if $library.lib == "paired":
23 #if $library.filter: 24 #if $library.filter:
24 && python '$__tool_directory__/FilterUncorrectabledPEfastq.py' 25 && python '$__tool_directory__/FilterUncorrectabledPEfastq.py'
25 -1 output_file_directory/input_1.cor.fq -2 output_file_directory/input_2.cor.fq -o fixed 2>&1 > rmunfixable.log && cat rmunfixable.log 26 -1 output_file_directory/input_1.cor.fq -2 output_file_directory/input_2.cor.fq -o fixed 2>&1 > rmunfixable.log && cat rmunfixable.log
26 #end if 27 #end if
38 <when value="paired"> 39 <when value="paired">
39 <param type="data" name="input1" label="FastQ file R1 (left)" format="fastq,fastqsanger" /> 40 <param type="data" name="input1" label="FastQ file R1 (left)" format="fastq,fastqsanger" />
40 <param type="data" name="input2" label="FastQ file R2 (right)" format="fastq,fastqsanger" /> 41 <param type="data" name="input2" label="FastQ file R2 (right)" format="fastq,fastqsanger" />
41 <param name="filter" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Filter uncorrectable reads" help="This will run FilterUncorrectabledPEfastq and remove uncorrectable reads."/> 42 <param name="filter" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Filter uncorrectable reads" help="This will run FilterUncorrectabledPEfastq and remove uncorrectable reads."/>
42 </when> 43 </when>
43 </conditional> 44 </conditional>
44 <conditional name="advanced"> 45 <conditional name="advanced">
45 <param name="adv" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Additional options"/> 46 <param name="adv" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Additional options"/>
46 <when value="TRUE"> 47 <when value="TRUE">
47 <param name="kmers" label="kmer length" value="23" max="32" type="integer" help="(smaller 33, default: 23)"/> 48 <param name="kmers" label="kmer length" value="23" max="32" type="integer" help="(smaller 33, default: 23)"/>
48 <param name="maxcorK" label="max correction within k-bp window" value="4" type="integer" help="the maximum number of correction within k-bp window (default: 4)"/> 49 <param name="maxcorK" label="max correction within k-bp window" value="4" type="integer" help="the maximum number of correction within k-bp window (default: 4)"/>
53 <param name="kmers" value="23" type="hidden"/> 54 <param name="kmers" value="23" type="hidden"/>
54 <param name="maxcorK" value="4" type="hidden"/> 55 <param name="maxcorK" value="4" type="hidden"/>
55 <param name="wk" value="0.95" type="hidden"/> 56 <param name="wk" value="0.95" type="hidden"/>
56 <param name="ek" value="100000000" type="hidden"/> 57 <param name="ek" value="100000000" type="hidden"/>
57 </when> 58 </when>
58 </conditional> 59 </conditional>
59 </inputs> 60 </inputs>
60 <outputs> 61 <outputs>
61 <data name="output1" format="fastq" label="${tool.name} on ${on_string}" from_work_dir="output_file_directory/input_1.cor.fq"> 62 <data name="output1" format="fastq" label="${tool.name} on ${on_string}" from_work_dir="output_file_directory/input_1.cor.fq">
62 <filter>library['lib'] == 'single'</filter> 63 <filter>library['lib'] == 'single'</filter>
63 </data> 64 </data>
64 <data name="output2" format="fastq" label="${tool.name} on ${on_string}: cor R1" from_work_dir="output_file_directory/input_1.cor.fq"> 65 <data name="output2" format="fastq" label="${tool.name} on ${on_string}: cor R1" from_work_dir="output_file_directory/input_1.cor.fq">
65 <filter>library['lib'] == 'paired' and library['filter'] is False</filter> 66 <filter>library['lib'] == 'paired' and library['filter'] is False</filter>
66 </data> 67 </data>
67 <data name="output3" format="fastq" label="${tool.name} on ${on_string}: cor R2" from_work_dir="output_file_directory/input_2.cor.fq"> 68 <data name="output3" format="fastq" label="${tool.name} on ${on_string}: cor R2" from_work_dir="output_file_directory/input_2.cor.fq">
68 <filter>library['lib'] == 'paired' and library['filter'] is False</filter> 69 <filter>library['lib'] == 'paired' and library['filter'] is False</filter>
69 </data> 70 </data>
70 <data name="output4" format="fastq" label="${tool.name} on ${on_string}: fixed R1" from_work_dir="fixed_input_1.cor.fq"> 71 <data name="output4" format="fastq" label="${tool.name} on ${on_string}: fixed R1" from_work_dir="fixed_input_1.cor.fq">
71 <filter>library['lib'] == 'paired' and library['filter']</filter> 72 <filter>library['lib'] == 'paired' and library['filter']</filter>
72 </data> 73 </data>
73 <data name="output5" format="fastq" label="${tool.name} on ${on_string}: fixed R2" from_work_dir="fixed_input_2.cor.fq"> 74 <data name="output5" format="fastq" label="${tool.name} on ${on_string}: fixed R2" from_work_dir="fixed_input_2.cor.fq">
74 <filter>library['lib'] == 'paired' and library['filter']</filter> 75 <filter>library['lib'] == 'paired' and library['filter']</filter>
75 </data> 76 </data>
76 </outputs> 77 </outputs>
77 <tests> 78 <tests>
78 <test> 79 <test>
79 <conditional name="library"> 80 <conditional name="library">
80 <param name="lib" value="paired"/> 81 <param name="lib" value="paired"/>