Mercurial > repos > iuc > khmer_normalize_by_median

annotate normalize-by-median.xml @ 10:4d23ab83ea29 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 238d0992c63de53623c4fc05eec8bd8d67001997
author iuc
date Thu, 03 Oct 2024 13:46:42 +0000
parents b1fe2ef3d244
children
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1 <tool id="khmer_normalize_by_median" name="khmer: Normalize By Median" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>Filter reads using digital normalization via 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="bio_tools"/>
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8 <expand macro="requirements" />
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9 <expand macro="stdio" />
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10 <expand macro="version" />
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11 <command><![CDATA[
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12 #import re
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13 set -u &&
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14 mkdir output &&
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16 @LINK_SEQUENCES@
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17 cd output/ &&
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18 normalize-by-median.py
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19 ${paired_switch}
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20 ${force_single_switch}
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21 @TABLEPARAMS@
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22 --cutoff=${cutoff}
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23 #if $unpaired_reads_filename
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24 --unpaired-reads=${unpaired_reads_filename}
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25 #end if
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26 #if $save_countgraph
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27 --savegraph=${countgraph}
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28 #end if
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29 #if $countgraph_to_load
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30 --loadgraph=${countgraph_to_load}
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31 #end if
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32 --report=${report}
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33 $gzip
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34 @USE_SEQUENCES@
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35 ]]>
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36 </command>
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37 <inputs>
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38 <expand macro="input_sequences_filenames" />
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39 <param argument="--paired" name="paired_switch" type="boolean" checked="false" truevalue="--paired" falsevalue=""
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40 label="Require all sequences be properly paired?"
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41 help="The tool will fail if given improperly paired reads and this option is selected." />
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42 <param argument="--force_single" name="force_single_switch" type="boolean" checked="false" truevalue="--force_single" falsevalue=""
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43 label="Ignore all pairing information?"
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44 help="By default this tool process reads in a pair-aware manner. This option disables that behavior." />
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45 <param argument="--unpaired-reads" name="unpaired_reads_filename" type="data" format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina" optional="true"
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46 label="Extra unpaired reads"
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47 help="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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48 <param argument="--loadgraph" name="countgraph_to_load" type="data" format="oxlicg" optional="true"
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49 label="Optional k-mer countgraph"
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50 help="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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51 <param argument="--savegraph" name="save_countgraph" type="boolean" label="Save the k-mer countgraph(s) in a file" help="" />
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52 <param argument="--cutoff" type="integer" min="1" value="20" label="Cutoff" help="" />
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53 <expand macro="tableinputs" />
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54 </inputs>
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55 <outputs>
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56 <data name="countgraph" format="oxlicg" label="${tool.name} on ${on_string}: k-mer countgraph">
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57 <filter>save_countgraph == True</filter>
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58 </data>
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59 <data name="report" format="csv" label="${tool.name} on ${on_string}: report" />
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60 <expand macro="output_sequences" extension="keep"/>
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61 </outputs>
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62 <tests>
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63 <test expect_num_outputs="2">
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64 <param name="inputs" value="test-abund-read-2.fa" ftype="fasta"/>
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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="test-abund-read-2.fa" ftype="fasta">
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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 expect_num_outputs="2">
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78 <param name="inputs" value="test-abund-read-2.fa.gz" ftype="fasta.gz"/>
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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="test-abund-read-2.fa.gz" ftype="fasta.gz">
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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>
10
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92 <test expect_num_outputs="3">
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93 <param name="inputs" value="test-abund-read-paired.fa" ftype="fasta"/>
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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 <param name="save_countgraph" value="true"/>
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99 <output name="report" file="normalize-by-median.paired.report.txt" />
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100 <output_collection name="sequences" type="list">
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101 <element name="test-abund-read-paired.fa" ftype="fasta">
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102 <assert_contents>
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103 <has_text text="GGTTGACGGGGCTCAGGGGG" />
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104 <has_text text="GGTTGACGGGGCTCAGGG" />
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105 </assert_contents>
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106 </element>
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107 </output_collection>
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108 <output name="countgraph">
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109 <assert_contents>
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110 <has_size size="1k"/>
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111 </assert_contents>
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112 </output>
0
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113 </test>
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114 </tests>
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115 <help><![CDATA[
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116 Do digital normalization (remove mostly redundant sequences)
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117
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118 Discard sequences based on whether or not their median k-mer abundance lies
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119 above a specified cutoff. Kept sequences will be placed in <fileN>.keep.
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120
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121 By default, Paired end reads will be considered together; if either read will
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122 be kept, then both will be kept. (This keeps both reads from a fragment, and
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123 helps with retention of repeats.) Unpaired reads are treated individually.
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124
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125 If `--paired` is set then proper pairing is required and the tool will exit on
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126 unpaired reads, although `--unpaired-reads` can be used to supply a file of
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127 orphan reads to be read after the paired reads.
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128
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129 `--force_single` will ignore all pairing information and treat reads
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130 individually.
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131
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132 With `-s`/`--savegraph`, the k-mer countgraph will be saved to the specified
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133 file after all sequences have been processed. `--loadgraph` will load the
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134 specified k-mer countgraph before processing the specified files. Note
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135 that the countgraph is in same format as those produced by
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136 `load-into-counting.py` and consumed by `abundance-dist.py`.
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137
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138 @HELP_FOOTER@
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139 ]]>
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140 </help>
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141 <citations>
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142 <expand macro="software-citation" />
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143 <expand macro="diginorm-citation" />
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144 </citations>
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145 </tool>