Mercurial > repos > nilesh > rseqc

annotate read_hexamer.xml @ 14:b21f0167e197 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit ccb6f7edba5492f4750ef8a59c4f91eb67fdbbec
author iuc
date Wed, 22 Feb 2023 15:05:13 +0000
parents a7f9084572fe
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a7f9084572fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
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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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11 <expand macro="stdio" />
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13 <version_command><![CDATA[read_hexamer.py --version]]></version_command>
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15 <command><![CDATA[
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16 #import re
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17 #set $input_list = []
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18 #for $i, $input in enumerate($inputs):
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20 #set $safename = re.sub('[^\w\-_]', '_', $input.element_identifier)
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21 #if $safename in $input_list:
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22 #set $safename = str($safename) + "." + str($i)
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23 #end if
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24 $input_list.append($safename)
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26 #if $input.is_of_type("fastq.gz", "fastqsanger.gz"):
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27 gunzip -c '${input}' > "${safename}" &&
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28 #else:
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29 ln -sf '${input}' "${safename}" &&
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30 #end if
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31 #end for
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32 read_hexamer.py -i '${ ','.join( [ $name for $name in $input_list ] ) }'
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33 #if $refgenome:
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34 -r '${refgenome}'
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35 #end if
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36 #if $refgene:
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37 -g '${refgene}'
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38 #end if
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39 > '${output}'
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40 ]]>
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41 </command>
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43 <inputs>
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44 <param name="inputs" type="data" label="Read sequences in fasta or fastq format" format="fasta,fastq,fastqsanger,fastq.gz,fastqsanger.gz" help="(--input)" multiple="true" />
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45 <param name="refgenome" type="data" label="Reference genome seqeunce (fasta)" format="fasta" optional="true" help="(--refgenome)" />
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46 <param name="refgene" type="data" label="Reference mRNA sequence (fasta)" format="fasta" optional="true" help="(--refgene)" />
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47 </inputs>
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49 <outputs>
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50 <data name="output" format="tabular" label="${tool.name} on ${on_string}" />
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51 </outputs>
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52
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53 <tests>
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54 <test>
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55 <param name="inputs" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.R1.fastq"/>
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56 <output name="output">
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57 <assert_contents>
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58 <has_line line="Hexamer&#009;pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq" />
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59 <has_text text="0.002173913043478261" />
3
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60 </assert_contents>
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61 </output>
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62 </test>
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63 <test>
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64 <param name="inputs" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.R1.fastq.gz" ftype="fastqsanger.gz"/>
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65 <output name="output">
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66 <assert_contents>
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67 <has_line line="Hexamer&#009;pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq_gz" />
13
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68 <has_text text="0.002173913043478261" />
3
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69 </assert_contents>
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70 </output>
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71 </test>
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72 <test>
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73 <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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74 <output name="output">
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75 <assert_contents>
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76 <has_line line="Hexamer&#009;pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq&#009;pairend_strandspecific_51mer_hg19_chr1_1-100000_R2_fastq" />
13
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77 <has_text text="0.002173913043478261" />
3
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78 </assert_contents>
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79 </output>
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80 </test>
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81 <test>
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82 <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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83 <output name="output">
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84 <assert_contents>
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85 <has_line line="Hexamer&#009;pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq&#009;pairend_strandspecific_51mer_hg19_chr1_1-100000_R1_fastq.1" />
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86 <has_text text="0.002173913043478261" />
3
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87 </assert_contents>
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88 </output>
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89 </test>
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90 <!-- Unable to test with collections at the moment (requires type="data_collection" on the input)
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91 <test>
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92 <param name="inputs">
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93 <collection type="list">
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94 <element name="read_1" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.R1.fastq" />
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95 <element name="read_2" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.R2.fastq" />
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96 </collection>
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97 </param>
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98 <output name="output" file="output.read_hexamer.2.txt" />
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99 </test>
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100 -->
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101 </tests>
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102
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103 <help><![CDATA[
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104 read_hexamer.py
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105 +++++++++++++++++++++
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106
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107 Calculate hexamer (6mer) frequency. If ‘-r’ was specified, hexamer frequency
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108 is also calculated for the reference genome. If ‘-g’ was provided, hexamer
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109 frequency is also calculated for the mRNA sequences.
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110
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111 Inputs
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112 ++++++++++++++
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113
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114 Input reads file
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115 Read sequences in fasta or fastq format.
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116
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117 Reference Genome
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118 Reference genome sequence in fasta format.
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119
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120 Reference Gene
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121 Reference mRNA sequences in fasta format.
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122
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123
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124 Outputs
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125 ++++++++++++++
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126
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127 Tabular file of hexamer frequences in for each input.
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128
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129 @ABOUT@
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130
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131 ]]>
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132 </help>
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133
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134 <expand macro="citations" />
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135
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136 </tool>