Mercurial > repos > iuc > khmer_filter_below_abundance_cutoff

annotate filter-below-abund.xml @ 9:19607c740d19 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7599ef16dc8b83ee49236ed5bb229260c969b0ab
author iuc
date Mon, 17 Jun 2024 11:47:14 +0000
parents b469ab47b490
children
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b469ab47b490 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 14ea2dc5ef36219c908ed64b256794711ce7b902"
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1 <tool id="khmer_filter_below_abundance_cutoff" name="khmer: Filter reads" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>
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e0e33e40d7c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit 72078bced0c08685219c6e80e42ce07458822391
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3 below k-mer abundance of 50
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67b597ec0baf planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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4 </description>
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5 <expand macro="bio_tools"/>
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6 <macros>
67b597ec0baf planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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7 <token name="@BINARY@">filter-below-abund.py</token>
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8 <import>macros.xml</import>
67b597ec0baf planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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9 </macros>
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10 <expand macro="requirements">
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11 <requirement type="package" version="1.0.1">screed</requirement>
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12 </expand>
0
67b597ec0baf planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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13 <expand macro="stdio" />
67b597ec0baf planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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14 <command><![CDATA[
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15 @LINK_SEQUENCES@
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16 mkdir output &&
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17 cd output &&
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18 python '$__tool_directory__/@BINARY@'
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19 '${input_countgraph_filename}'
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20 @USE_SEQUENCES@
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21 > '$log'
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22 ]]>
0
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23 </command>
67b597ec0baf planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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24 <inputs>
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25 <expand macro="input_sequences_filenames" />
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26 <expand macro="input_countgraph_filename" />
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27 </inputs>
67b597ec0baf planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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28 <outputs>
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29 <data name="log" format="txt" />
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30 <expand macro="output_sequences" extension="below"/>
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31 </outputs>
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32 <tests>
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33 <test>
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34 <param name="inputs" value="test-abund-read-2.fa" />
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35 <param name="input_countgraph_filename" value="test-abund-read-2.large.oxlicg" ftype="oxlicg" />
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36 <output_collection name="sequences">
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37 <element name="test-abund-read-2.fa" file="test-abund-read-2.fa.below" />
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38 </output_collection>
67b597ec0baf planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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39 </test>
67b597ec0baf planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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40 </tests>
67b597ec0baf planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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41 <help><![CDATA[
67b597ec0baf planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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42 Trims fastq/fasta sequences at k-mers with abundance below 50 based on a provided k-mer countgraph.
67b597ec0baf planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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43
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44 @HELP_FOOTER@
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45 ]]></help>
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46 <citations>
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47 <expand macro="software-citation" />
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48 <expand macro="counting-citation" />
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49 </citations>
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50 </tool>