annotate count-median.xml @ 7:77410799e8e9 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
author iuc
date Wed, 18 Dec 2019 16:02:57 -0500
parents 84b323860b0a
children 06d1d91c67e5
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77410799e8e9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
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1 <tool id="khmer_count_median" name="khmer: Count Median" version="@WRAPPER_VERSION@@TOOL_VERSION@">
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2 <description>Count the median/avg k-mer abundance for each sequence</description>
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3 <macros>
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4 <token name="@BINARY@">count-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[
7
77410799e8e9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
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11 set -u &&
0
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12 @BINARY@
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13 $input_countgraph_filename
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14 $input_sequence_filename
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15 $output_summary_filename
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16 ]]>
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17 </command>
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18 <inputs>
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19 <expand macro="input_sequence_filename" />
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20 <expand macro="input_countgraph_filename" />
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21 </inputs>
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22 <outputs>
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23 <data name="output_summary_filename" format="txt"
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77410799e8e9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
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24 label="${tool.name} on ${on_string}" />
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25 </outputs>
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26 <tests>
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27 <test>
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28 <param name="input_sequence_filename" value="test-abund-read-2.fa" />
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29 <param name="input_countgraph_filename" value="test-abund-read-2.oxlicg" ftype="oxlicg" />
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30 <output name="output_summary_filename">
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31 <assert_contents>
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32 <has_text text="seq,1001,1001.0,0.0,18" />
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33 <has_text text="895:1:37:17593:9954/1,1,21.408163071,141.391921997,114" />
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34 </assert_contents>
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35 </output>
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36 </test>
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37 </tests>
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38 <help><![CDATA[
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39 Count the median/avg k-mer abundance for each sequence in the input file,
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40 based on the k-mer counts in the given k-mer countgraph. Can be used to
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41 estimate expression levels (mRNAseq) or coverage (genomic/metagenomic). The
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42 output file contains sequence id, median, average, stddev, and seq length;
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43 fields are separated by spaces. For khmer 1.x count-median.py will split
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44 sequence names at the first space which means that some sequence formats (e.g.
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45 paired FASTQ in Casava 1.8 format) will yield uninformative names. Use
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46 `--csv` to fix this behavior.
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47
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48 @HELP_FOOTER@
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49 ]]>
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50 </help>
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51 <citations>
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52 <expand macro="software-citation" />
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53 <expand macro="diginorm-citation" />
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54 </citations>
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55 </tool>