Mercurial > repos > iuc > khmer_normalize_by_median

annotate normalize-by-median.xml @ 0:5531deeabd2c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
author iuc
date Wed, 11 Nov 2015 09:46:18 -0500
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children 73314e26dcfd
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5531deeabd2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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1 <tool id="khmer_normalize_by_median" name="Normalize By Median" version="@WRAPPER_VERSION@.0">
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2 <description>Filters a fastq/fasta file using digital normalization via median k-mer abundances</description>
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3 <macros>
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4 <token name="@BINARY@">normalize-by-median.py</token>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <expand macro="stdio" />
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9 <expand macro="version" />
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10 <command><![CDATA[
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11 set -xu &&
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12 #for $num, $input in enumerate($inputs)
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13 ln -s ${input} sequence-${num} &&
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14 #end for
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15 mkdir output &&
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16 cd output &&
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17 normalize-by-median.py
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18 ${paired_switch}
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19 ${force_single_switch}
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20 @TABLEPARAMS@
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21 --cutoff=${cutoff}
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22 #if $unpaired_reads_filename
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23 --unpaired-reads=${unpaired_reads_filename}
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24 #end if
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25 #if $save_countgraph
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26 --savegraph=${countgraph}
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27 #end if
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28 #if $countgraph_to_load
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29 --loadgraph=${countgraph_to_load}
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30 #end if
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31 --report=${report}
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32 ../sequence-*
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33 ]]>
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34 </command>
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35 <inputs>
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36 <expand macro="input_sequences_filenames" />
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37 <param name="paired_switch" type="boolean" checked="false" truevalue="--paired" falsevalue=""
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38 label="Require all sequences be properly paired?"
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39 help="(--paired) The tool will fail if given improperly paired reads and this option is selected." />
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40 <param name="force_single_switch" type="boolean" checked="false" truevalue="--force_single" falsevalue=""
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41 label="Ignore all pairing information?"
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42 help="(--paired) By default this tool process reads in a pair-aware manner. This option disables that behavior." />
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43 <param name="unpaired_reads_filename" type="data" format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina" optional="true"
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44 label="Extra unpaired reads"
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45 help="(--unpaired-reads) If all but one of your sequence files are interleaved paired end reads you can include one unpaired file to be processed last without regard to pairing." />
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46 <param name="countgraph_to_load" type="data" format="oxlicg" optional="true"
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47 label="Optional k-mer countgraph"
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48 help="(--loadgraph) The inputs file(s) will be processed using the kmer counts in the specified k-mer countgraph file as a starting point." />
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49 <param name="save_countgraph" type="boolean" label="Save the k-mer countgraph(s) in a file" help="(--savegraph)" />
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50 <param name="cutoff" type="integer" min="1" value="20" label="Cutoff" help="(--cutoff)" />
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51 <expand macro="tableinputs" />
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52 </inputs>
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53 <outputs>
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54 <data name="countgraph" format="oxlicg" label="${tool.name} k-mer countgraph">
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55 <filter>save_countgraph == True</filter>
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56 </data>
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57 <data name="report" format="txt" label="${tool.name} report" />
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58 <collection name="sequences" type="list">
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59 <discover_datasets pattern="__name__" directory="output" />
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60 </collection>
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61 </outputs>
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62 <tests>
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63 <test>
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64 <param name="inputs" value="test-abund-read-2.fa"/>
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65 <param name="type" value="specific" />
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66 <param name="cutoff" value="1" />
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67 <param name="ksize" value="17" />
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68 <output name="report" file="normalize-by-median.report.txt" />
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69 <output_collection name="sequences" type="list">
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70 <element name="sequence-0.keep">
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71 <assert_contents>
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72 <has_text text="GGTTGACGGGGCTCAGGGGG" />
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73 </assert_contents>
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74 </element>
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75 </output_collection>
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76 </test>
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77 <test>
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78 <param name="inputs" value="test-abund-read-2.fa" />
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79 <param name="type" value="specific" />
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80 <param name="cutoff" value="2" />
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81 <param name="ksize" value="17" />
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82 <output name="report" file="normalize-by-median.c2.report.txt" />
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83 <output_collection name="sequences" type="list">
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84 <element name="sequence-0.keep">
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85 <assert_contents>
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86 <has_text text="GGTTGACGGGGCTCAGGGGG" />
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87 <has_text text="GGTTGACGGGGCTCAGGG" />
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88 </assert_contents>
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89 </element>
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90 </output_collection>
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91 </test>
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92 <test>
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93 <param name="inputs" value="test-abund-read-paired.fa" />
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94 <param name="type" value="specific" />
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95 <param name="cutoff" value="1" />
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96 <param name="ksize" value="17" />
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97 <param name="paired" value="true" />
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98 <output name="report" file="normalize-by-median.paired.report.txt" />
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99 <output_collection name="sequences" type="list">
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100 <element name="sequence-0.keep">
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101 <assert_contents>
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102 <has_text text="GGTTGACGGGGCTCAGGGGG" />
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103 <has_text text="GGTTGACGGGGCTCAGGG" />
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104 </assert_contents>
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105 </element>
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106 </output_collection>
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107 </test>
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108 </tests>
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109 <help><![CDATA[
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110 Do digital normalization (remove mostly redundant sequences)
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111
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112 Discard sequences based on whether or not their median k-mer abundance lies
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113 above a specified cutoff. Kept sequences will be placed in <fileN>.keep.
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114
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115 By default, Paired end reads will be considered together; if either read will
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116 be kept, then both will be kept. (This keeps both reads from a fragment, and
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117 helps with retention of repeats.) Unpaired reads are treated individually.
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118
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119 If `--paired` is set then proper pairing is required and the tool will exit on
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120 unpaired reads, although `--unpaired-reads` can be used to supply a file of
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121 orphan reads to be read after the paired reads.
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122
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123 `--force_single` will ignore all pairing information and treat reads
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124 individually.
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125
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126 With `-s`/`--savegraph`, the k-mer countgraph will be saved to the specified
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127 file after all sequences have been processed. `--loadgraph` will load the
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128 specified k-mer countgraph before processing the specified files. Note
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129 that the countgraph is in same format as those produced by
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130 `load-into-counting.py` and consumed by `abundance-dist.py`.
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131
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132 @HELP_FOOTER@
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133 ]]>
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134 </help>
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135 <citations>
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136 <expand macro="software-citation" />
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137 <expand macro="diginorm-citation" />
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138 </citations>
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139 </tool>