Mercurial > repos > iuc > obi_illumina_pairend

comparison illuminapairedend.xml @ 3:83fbdf93d51e draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
author iuc
date Mon, 10 May 2021 19:36:09 +0000
parents 0c9296704212
children 8cb6bd511879
comparison
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2:94f412098ac8 3:83fbdf93d51e
1 <tool id="obi_illumina_pairend" name="Illuminapairedend - Assembling pair-end reads" version="@TOOL_VERSION@"> 1 <tool id="obi_illumina_pairend" name="Illuminapairedend" version="@TOOL_VERSION@" profile="@PROFILE@">
2 <description>Construct consensus reads from Illumina pair-end reads</description> 2 <description>Construct consensus reads from Illumina pair-end reads</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> 8 <command>
9 <![CDATA[
10 #if $inputfastq3p.ext.endswith(".gz")
11 gunzip -c '$inputfastq3p' > fastq3p.fastq &&
12 gunzip -c '$inputfastq5p' > fastq5p.fastq &&
13 #else
14 ln -s '$inputfastq3p' fastq3p.fastq &&
15 ln -s '$inputfastq5p' fastq5p.fastq &&
16 #end if
9 17
10 <![CDATA[
11 illuminapairedend 18 illuminapairedend
12 19 ##--index-file=
20 #if $inputfastq3p.ext.startswith("fastqsolexa")
21 ##input file is in fastq nucleic format produced by solexa sequencer
22 --solexa
23 #else if $inputfastq3p.ext.startswith("fastqillumina")
24 ##input file is in fastq nucleic format produced by solexa sequencer
25 --illumina
26 #else
27 ## input file is in sanger fastq nucleic format (standard fastq)
28 --sanger
29 #end if
30 --without-progress-bar
13 --score-min='$score' 31 --score-min='$score'
14 -r '$inputfastq3p' 32 -r fastq3p.fastq
15 '$inputfastq5p' > '$output' 33 fastq5p.fastq
16 34 #if $inputfastq3p.ext.endswith(".gz")
35 | gzip -c
36 #end if
37 > '$output'
17 ]]> 38 ]]>
18
19 </command> 39 </command>
20
21 <inputs> 40 <inputs>
22 <param name="inputfastq3p" type="data" format="fastq" label="Read from file" help="file of 3p (1:) Illumina pair-end reads to assemble in sanger fastq nucleic format (standard fastq)" /> 41 <param name="inputfastq3p" type="data" format="fastq,fastq.gz" label="Read from file" help="file of 3p (1:) Illumina pair-end reads to assemble in sanger fastq nucleic format (standard fastq)" />
23 <param name="inputfastq5p" type="data" format="fastq" label="Read from file" help="file of 5p (2:) Illumina pair-end reads to assemble in sanger fastq nucleic format (standard fastq)" /> 42 <param name="inputfastq5p" type="data" format="fastq,fastq.gz" label="Read from file" help="file of 5p (2:) Illumina pair-end reads to assemble in sanger fastq nucleic format (standard fastq)" />
24 <param name="score" type="float" value="40.0" label="minimum score for keeping aligment"/> 43 <param name="score" type="float" value="40.0" label="minimum score for keeping aligment"/>
25 </inputs> 44 </inputs>
26 <outputs> 45 <outputs>
27 <data format="fastq" name="output" label="${tool.name} on ${on_string}: assembly results" /> 46 <data name="output" format_source="inputfastq3p" label="${tool.name} on ${on_string}: assembly results" />
28 </outputs> 47 </outputs>
29 48
30 <tests> 49 <tests>
31 <test> 50 <test>
32 <param name="inputfastq3p" value="wolf_small.F.fastq" /> 51 <param name="inputfastq3p" value="wolf_small.F.fastq" ftype="fastqsanger" />
33 <param name="inputfastq5p" value="wolf_small.R.fastq" /> 52 <param name="inputfastq5p" value="wolf_small.R.fastq" ftype="fastqsanger" />
34 <param name="score" value="40.0" /> 53 <param name="score" value="40.0" />
35 <output name="output" file="illuminapairedend.output.fastq" ftype="fastq"/> 54 <output name="output" file="illuminapairedend.output.fastq" ftype="fastqsanger" />
55 </test>
56 <test>
57 <param name="inputfastq3p" value="wolf_small.F.fastq.gz" ftype="fastqsanger.gz" />
58 <param name="inputfastq5p" value="wolf_small.R.fastq.gz" ftype="fastqsanger.gz" />
59 <param name="score" value="40.0" />
60 <output name="output" file="illuminapairedend.output.fastq.gz" ftype="fastqsanger.gz" decompress="true"/>
36 </test> 61 </test>
37 </tests> 62 </tests>
38 63
39 <help><![CDATA[ 64 <help><![CDATA[
40 65