Mercurial > repos > nilesh > rseqc

annotate read_hexamer.xml @ 63:27e16a30667a draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de
author iuc
date Tue, 09 Apr 2024 11:24:55 +0000
parents 5968573462fa
children
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1 <tool id="rseqc_read_hexamer" name="Hexamer frequency" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
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2 <description>
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3 calculates hexamer (6mer) frequency for reads, genomes, and mRNA sequences
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4 </description>
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5 <macros>
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6 <import>rseqc_macros.xml</import>
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7 </macros>
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8 <expand macro="bio_tools"/>
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9 <expand macro="requirements"/>
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10 <expand macro="stdio"/>
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11 <version_command><![CDATA[read_hexamer.py --version]]></version_command>
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12 <command><![CDATA[
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13 #import re
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14 #set $input_list = []
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15 #for $i, $input in enumerate($inputs):
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17 #set $safename = re.sub('[^\w\-_]', '_', $input.element_identifier)
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18 #if $safename in $input_list:
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19 #set $safename = str($safename) + "." + str($i)
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20 #end if
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21 $input_list.append($safename)
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23 #if $input.is_of_type("fastq.gz", "fastqsanger.gz"):
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24 gunzip -c '${input}' > "${safename}" &&
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25 #else:
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26 ln -sf '${input}' "${safename}" &&
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27 #end if
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28 #end for
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29 read_hexamer.py -i '${ ','.join( [ $name for $name in $input_list ] ) }'
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30 #if $refgenome:
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31 -r '${refgenome}'
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32 #end if
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33 #if $refgene:
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34 -g '${refgene}'
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35 #end if
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36 > '${output}'
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37 ]]>
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38 </command>
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39 <inputs>
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40 <param name="inputs" type="data" label="Read sequences in fasta or fastq format" format="fasta,fastq,fastqsanger,fastq.gz,fastqsanger.gz" help="(--input)" multiple="true"/>
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41 <param name="refgenome" type="data" label="Reference genome seqeunce (fasta)" format="fasta" optional="true" help="(--refgenome)"/>
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42 <param name="refgene" type="data" label="Reference mRNA sequence (fasta)" format="fasta" optional="true" help="(--refgene)"/>
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43 </inputs>
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44 <outputs>
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45 <data name="output" format="tabular" label="${tool.name} on ${on_string}"/>
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46 </outputs>
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47 <tests>
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48 <test expect_num_outputs="1">
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49 <param name="inputs" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.R1.fastq"/>
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50 <output name="output">
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51 <assert_contents>
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52 <has_line line="Hexamer&#9;pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq"/>
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53 <has_text text="0.002173913043478261"/>
51
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54 </assert_contents>
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55 </output>
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56 </test>
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57 <test expect_num_outputs="1">
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58 <param name="inputs" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.R1.fastq.gz" ftype="fastqsanger.gz"/>
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59 <output name="output">
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60 <assert_contents>
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61 <has_line line="Hexamer&#9;pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq_gz"/>
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62 <has_text text="0.002173913043478261"/>
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63 </assert_contents>
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64 </output>
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65 </test>
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66 <test expect_num_outputs="1">
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67 <param name="inputs" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.R1.fastq,pairend_strandspecific_51mer_hg19_chr1_1-100000.R2.fastq"/>
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68 <output name="output">
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69 <assert_contents>
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70 <has_line line="Hexamer&#9;pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq&#9;pairend_strandspecific_51mer_hg19_chr1_1-100000_R2_fastq"/>
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71 <has_text text="0.002173913043478261"/>
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72 </assert_contents>
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73 </output>
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74 </test>
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75 <test expect_num_outputs="1">
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76 <param name="inputs" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.R1.fastq,pairend_strandspecific_51mer_hg19_chr1_1-100000.R1.fastq"/>
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77 <output name="output">
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78 <assert_contents>
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79 <has_line line="Hexamer&#9;pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq&#9;pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq.1"/>
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80 <has_text text="0.002173913043478261"/>
51
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81 </assert_contents>
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82 </output>
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83 </test>
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84 <!-- Unable to test with collections at the moment (requires type="data_collection" on the input)
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85 <test>
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86 <param name="inputs">
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87 <collection type="list">
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88 <element name="read_1" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.R1.fastq" />
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89 <element name="read_2" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.R2.fastq" />
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90 </collection>
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91 </param>
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92 <output name="output" file="output.read_hexamer.2.txt" />
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93 </test>
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94 -->
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95 </tests>
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96 <help><![CDATA[
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97 read_hexamer.py
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98 +++++++++++++++++++++
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99
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100 Calculate hexamer (6mer) frequency. If ‘-r’ was specified, hexamer frequency
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101 is also calculated for the reference genome. If ‘-g’ was provided, hexamer
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102 frequency is also calculated for the mRNA sequences.
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103
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104 Inputs
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105 ++++++++++++++
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106
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107 Input reads file
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108 Read sequences in fasta or fastq format.
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109
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110 Reference Genome
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111 Reference genome sequence in fasta format.
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112
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113 Reference Gene
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114 Reference mRNA sequences in fasta format.
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115
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116
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117 Outputs
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118 ++++++++++++++
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119
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120 Tabular file of hexamer frequences in for each input.
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121
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122 @ABOUT@
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123
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124 ]]>
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125 </help>
63
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126 <expand macro="citations"/>
51
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127 </tool>