annotate filter-abund.xml @ 5:a4970dfc331c draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 19ea4feff5ccf3744c549b9a67259947a1cb90ba
author iuc
date Sat, 21 Jan 2017 14:43:16 -0500
parents 03246d4ea8cd
children 8c6433857aa8
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1 <tool id="khmer_filter_abundance" name="Filter reads" version="@WRAPPER_VERSION@.0">
0
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2 <description>
1
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3 by minimal k-mer abundance
0
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4 </description>
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5 <macros>
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6 <token name="@BINARY@">filter-abund.py</token>
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7 <import>macros.xml</import>
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8 </macros>
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9 <expand macro="requirements" />
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10 <expand macro="stdio" />
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11 <expand macro="version" />
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12 <command><![CDATA[
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13 set -xu &&
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14 #for $num, $input in enumerate($inputs)
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15 ln -s ${input} filter-abund-sequence-${num} &&
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16 #end for
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17 mkdir output && cd output &&
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18 @BINARY@
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19 --cutoff=${cutoff}
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20 ${variable_coverage}
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21 @THREADS@
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22 ${input_countgraph_filename}
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23 ../filter-abund-sequence*
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24 ]]>
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25 </command>
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26 <inputs>
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27 <expand macro="input_sequences_filenames" />
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28 <param name="variable_coverage" type="boolean" checked="false" truevalue="--variable-coverage" falsevalue=""
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29 label="Variable coverage"
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30 help="Only trim when a sequence has high enough coverage; median abundance > 20 (--variable_coverage)" />
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31 <param name="cutoff" type="integer" value="2" label="Cutoff"
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32 help="Trim at k-mers below this abundance. (--cutoff)" />
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33 <expand macro="input_countgraph_filename" />
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34 </inputs>
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35 <outputs>
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36 <collection name="filter-abund-sequences" type="list">
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37 <discover_datasets pattern="__name__" directory="output" />
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38 </collection>
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39 </outputs>
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40 <tests>
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41 <test>
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42 <param name="inputs" value="test-abund-read-2.fa" />
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43 <param name="input_countgraph_filename"
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44 value="test-abund-read-2.oxlicg" ftype="oxlicg" />
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45 <output_collection name="filter-abund-sequences" type="list">
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46 <element name="filter-abund-sequence-0.abundfilt">
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47 <assert_contents>
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48 <has_text text="GGTTGACGGGGCTCAGGG" />
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49 </assert_contents>
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50 </element>
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51 </output_collection>
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52 </test>
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53 <test>
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54 <param name="inputs" value="test-abund-read-2.fa" />
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55 <param name="input_countgraph_filename"
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56 value="test-abund-read-2.oxlicg" ftype="oxlicg" />
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57 <param name="cutoff" value="1" />
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58 <output_collection name="filter-abund-sequences" type="list">
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59 <element name="filter-abund-sequence-0.abundfilt">
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60 <assert_contents>
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61 <has_text text="GGTTGACGGGGCTCAGGG" />
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62 </assert_contents>
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63 </element>
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64 </output_collection>
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65 </test>
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66 </tests>
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67 <help><![CDATA[
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68 Trims fastq/fasta sequences at k-mers of a given abundance based on a provided k-mer countgraph
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69
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70 If the input sequences are from RNAseq or metagenome sequencing then
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71 `--variable-coverage` should be used.
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72
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73 @HELP_FOOTER@
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74 ]]>
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75 </help>
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76 <citations>
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77 <expand macro="software-citation" />
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78 <expand macro="counting-citation" />
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79 </citations>
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80 </tool>