Mercurial > repos > iuc > rcorrector

comparison rcorrector.xml @ 0:9a0b65ad3c84 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
author iuc
date Thu, 13 Sep 2018 07:00:00 -0400
parents
children 6703b98884a2
comparison
equal deleted inserted replaced
-1:000000000000 0:9a0b65ad3c84
1 <tool id="rcorrector" name="RNA-seq Rcorrector" version="1.0.3">
2 <description>a kmer-based error correction method for RNA-seq data</description>
3 <requirements>
4 <requirement type="package" version="1.0.3">rcorrector</requirement>
5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[
7 #if $library.lib == "single":
8 ln -s '$library.input1' input_1.fq &&
9 #end if
10 #if $library.lib == "paired":
11 ln -s '$library.input1' input_1.fq && ln -s '$library.input2' input_2.fq &&
12 #end if
13 run_rcorrector.pl
14 #if $library.lib == "single":
15 -s input_1.fq
16 #end if
17 #if $library.lib == "paired":
18 -1 input_1.fq -2 input_2.fq
19 #end if
20 -k '$advanced.kmers' -t \${GALAXY_SLOTS:-4} -maxcorK '$advanced.maxcorK' -wk '$advanced.wk' -ek '$advanced.ek' -od output_file_directory
21
22 #if $library.lib == "paired":
23 #if $library.filter:
24 && python '$__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 #end if
27 #end if
28 ]]></command>
29 <inputs>
30 <conditional name="library">
31 <param name="lib" type="select" label="Is this library paired- or single-end?">
32 <option value="single">single</option>
33 <option value="paired" selected="True">paired</option>
34 </param>
35 <when value="single">
36 <param type="data" name="input1" label="FastQ file" format="fastq,fastqsanger" />
37 </when>
38 <when value="paired">
39 <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 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 </conditional>
44 <conditional name="advanced">
45 <param name="adv" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Additional options"/>
46 <when value="TRUE">
47 <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="wk" label="estimate weak kmer count" value="0.95" type="float" help="the proportion of kmers that are used to estimate weak kmer count threshold, lower for more divergent genome (default: 0.95)"/>
50 <param name="ek" label="expected number of kmers" value="100000000" type="integer" help="expected_number_of_kmers: does not affect the correctness of program but affect the memory usage (default: 100000000)"/>
51 </when>
52 <when value="FALSE">
53 <param name="kmers" value="23" type="hidden"/>
54 <param name="maxcorK" value="4" type="hidden"/>
55 <param name="wk" value="0.95" type="hidden"/>
56 <param name="ek" value="100000000" type="hidden"/>
57 </when>
58 </conditional>
59 </inputs>
60 <outputs>
61 <data name="output1" format="fastq" label="${tool.name} on ${on_string}" from_work_dir="output_file_directory/input_1.cor.fq">
62 <filter>library['lib'] == 'single'</filter>
63 </data>
64 <data name="output2" format="fastq" label="${tool.name} on ${on_string}: cor R1" from_work_dir="output_file_directory/input_1.cor.fq">
65 <filter>library['lib'] == 'paired' and library['filter'] is False</filter>
66 </data>
67 <data name="output3" format="fastq" label="${tool.name} on ${on_string}: cor R2" from_work_dir="output_file_directory/input_2.cor.fq">
68 <filter>library['lib'] == 'paired' and library['filter'] is False</filter>
69 </data>
70 <data name="output4" format="fastq" label="${tool.name} on ${on_string}: fixed R1" from_work_dir="fixed_input_1.cor.fq">
71 <filter>library['lib'] == 'paired' and library['filter']</filter>
72 </data>
73 <data name="output5" format="fastq" label="${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 </data>
76 </outputs>
77 <tests>
78 <test>
79 <conditional name="library">
80 <param name="lib" value="paired"/>
81 <param name="input1" value="sample_read1.fq" ftype="fastq"/>
82 <param name="input2" value="sample_read2.fq" ftype="fastq"/>
83 </conditional>
84 <conditional name="advanced">
85 <param name="kmers" value="23"/>
86 <param name="maxcorK" value="4"/>
87 <param name="wk" value="0.95"/>
88 <param name="ek" value="100000000"/>
89 </conditional>
90 <output name="output2" file="sample_read1.cor.fq" ftype="fastq"/>
91 <output name="output3" file="sample_read2.cor.fq" ftype="fastq"/>
92 </test>
93 <test>
94 <conditional name="library">
95 <param name="lib" value="paired"/>
96 <param name="input1" value="sample_read1.fq" ftype="fastq"/>
97 <param name="input2" value="sample_read2.fq" ftype="fastq"/>
98 <param name="filter" value="TRUE"/>
99 </conditional>
100 <conditional name="advanced">
101 <param name="kmers" value="23"/>
102 <param name="maxcorK" value="4"/>
103 <param name="wk" value="0.95"/>
104 <param name="ek" value="100000000"/>
105 </conditional>
106 <output name="output2" file="fixed_sample_read1.cor.fq" compare="sim_size"/>
107 <output name="output3" file="fixed_sample_read2.cor.fq" compare="sim_size"/>
108 </test>
109 </tests>
110 <help><![CDATA[
111
112 What is Rcorrector?
113
114 Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data.
115 Rcorrector can also be applied to other type of sequencing data where the read coverage is non-uniform, such as single-cell sequencing.
116
117 Uncorrectable paired-end reads can be removed using FilterUncorrectabledPEfastq.
118
119 More informations, see citations.
120
121 ]]>
122 </help>
123 <citations>
124 <citation type="doi">10.1186/s13742-015-0089-y</citation>
125 <citation type="bibtex">
126 @misc{githubFilterUncorrectabledPEfastq,
127 author = {Adam H. Freedman},
128 year = {2016},
129 title = {FilterUncorrectabledPEfastq},
130 publisher = {GitHub},
131 journal = {GitHub repository},
132 url = {https://github.com/harvardinformatics/TranscriptomeAssemblyTools/blob/master/FilterUncorrectabledPEfastq.py}
133 }
134 </citation>
135 </citations>
136 </tool>