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comparison velveth.xml @ 3:920677cd220f draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet commit ccce07eb8b612cbe09702214d3184b0085c055a8"
author iuc
date Sun, 24 Jan 2021 15:40:17 +0000
parents 8d09f8be269e
children
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2:8d09f8be269e 3:920677cd220f
1 <tool id="velveth" name="velveth" version="@WRAPPER_VERSION@.2"> 1 <tool id="velveth" name="velveth" version="@WRAPPER_VERSION@.3">
2 <description>Prepare a dataset for the Velvet velvetg Assembler</description> 2 <description>Prepare a dataset for the Velvet velvetg Assembler</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"/>
13 mkdir -p '${outfile.extra_files_path}' && 13 mkdir -p '${outfile.extra_files_path}' &&
14 velveth 14 velveth
15 '$outfile.extra_files_path' 15 '$outfile.extra_files_path'
16 $hash_length 16 $hash_length
17 #for $i in $inputs 17 #for $i in $inputs
18 -${i.input_type.input.ext} 18 -fmtAuto
19 ${i.input_type.read_type} 19 ${i.input_type.read_type}
20 #if str( $i.input_type.input_type_selector ) == "paireds": 20 #if str( $i.input_type.input_type_selector ) == "paireds":
21 -separate '${i.input_type.input}' '${i.input_type.input2}' 21 -separate '${i.input_type.input}' '${i.input_type.input2}'
22 #else if str( $i.input_type.input_type_selector ) == "pairedi": 22 #else if str( $i.input_type.input_type_selector ) == "pairedi":
23 -interleaved '${i.input_type.input}' 23 -interleaved '${i.input_type.input}'
24 #else: 24 #else:
25 '${i.input_type.input}' 25 '${i.input_type.input}'
26 #end if 26 #end if
27 #end for 27 #end for
28 $strand_specific 28 $strand_specific
29 ]]></command> 29 ]]></command>
30 <inputs> 30 <inputs>
31 <param label="Hash Length" name="hash_length" type="integer" value="21" min="11" max="191" help="k-mer length in base pairs of the words being hashed."/> 31 <param label="Hash Length" name="hash_length" type="integer" value="21" min="11" max="191" help="k-mer length in base pairs of the words being hashed."/>
32 <param name="strand_specific" type="boolean" checked="false" truevalue="-strand_specific" falsevalue="" label="Use strand specific transcriptome sequencing" help="If you are using a strand specific transcriptome sequencing protocol, you may wish to use this option for better results."/> 32 <param name="strand_specific" type="boolean" checked="false" truevalue="-strand_specific" falsevalue="" label="Use strand specific transcriptome sequencing" help="If you are using a strand specific transcriptome sequencing protocol, you may wish to use this option for better results."/>
33 <repeat name="inputs" title="Input Files"> 33 <repeat name="inputs" title="Input Files">
34 <conditional name="input_type"> 34 <conditional name="input_type">
35 <param name="input_type_selector" type="select" label="Choose the input type"> 35 <param name="input_type_selector" type="select" label="Choose the input type">
36 <option value="single" selected="true">Single ended</option> 36 <option value="single" selected="true">Single ended</option>
79 <param name="hash_length" value="21" /> 79 <param name="hash_length" value="21" />
80 <repeat name="inputs"> 80 <repeat name="inputs">
81 <conditional name="input_type"> 81 <conditional name="input_type">
82 <param name="input_type_selector" value="paireds" /> 82 <param name="input_type_selector" value="paireds" />
83 <param name="read_type" value="-shortPaired" /> 83 <param name="read_type" value="-shortPaired" />
84 <param name="input1" value="R1.fastq" ftype="fastq" /> 84 <param name="input1" value="R1.fastq" ftype="fastqsanger" />
85 <param name="input2" value="R2.fastq" ftype="fastq" /> 85 <param name="input2" value="R2.fastq" ftype="fastqsanger" />
86 </conditional> 86 </conditional>
87 </repeat> 87 </repeat>
88 <param name="strand_specific" value="" /> 88 <param name="strand_specific" value="" />
89 <output name="outfile" file="velveth_paireds.out"> 89 <output name="outfile" file="velveth_paireds.out">
90 <extra_files type="file" name='Sequences' value="velveth_paireds/Sequences" compare="diff" /> 90 <extra_files type="file" name='Sequences' value="velveth_paireds/Sequences" compare="diff" />
95 <param name="hash_length" value="21" /> 95 <param name="hash_length" value="21" />
96 <repeat name="inputs"> 96 <repeat name="inputs">
97 <conditional name="input_type"> 97 <conditional name="input_type">
98 <param name="input_type_selector" value="single" /> 98 <param name="input_type_selector" value="single" />
99 <param name="read_type" value="-short" /> 99 <param name="read_type" value="-short" />
100 <param name="input" value="R1.fastq" ftype="fastq" /> 100 <param name="input" value="R1.fastq" ftype="fastqillumina" />
101 </conditional> 101 </conditional>
102 </repeat> 102 </repeat>
103 <param name="strand_specific" value="" /> 103 <param name="strand_specific" value="" />
104 <output name="outfile" file="velveth_single.out"> 104 <output name="outfile" file="velveth_single.out">
105 <extra_files type="file" name='Sequences' value="velveth_single/Sequences" compare="diff" /> 105 <extra_files type="file" name='Sequences' value="velveth_single/Sequences" compare="diff" />