annotate count-median.xml @ 0:42fbb6359626 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
author iuc
date Wed, 11 Nov 2015 09:45:59 -0500
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children 84b323860b0a
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42fbb6359626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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1 <tool id="khmer_count_median" name="Count Median" version="@WRAPPER_VERSION@.0">
42fbb6359626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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2 <description>Count the median/avg k-mer abundance for each sequence in the input file</description>
42fbb6359626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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3 <macros>
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4 <token name="@BINARY@">count-median.py</token>
42fbb6359626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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5 <import>macros.xml</import>
42fbb6359626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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6 </macros>
42fbb6359626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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7 <expand macro="requirements" />
42fbb6359626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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8 <expand macro="stdio" />
42fbb6359626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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9 <expand macro="version" />
42fbb6359626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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10 <command><![CDATA[
42fbb6359626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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11 set -xu &&
42fbb6359626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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12 @BINARY@
42fbb6359626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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13 $input_countgraph_filename
42fbb6359626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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14 $input_sequence_filename
42fbb6359626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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15 $output_summary_filename
42fbb6359626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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16 ]]>
42fbb6359626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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17 </command>
42fbb6359626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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18 <inputs>
42fbb6359626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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19 <expand macro="input_sequence_filename" />
42fbb6359626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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20 <expand macro="input_countgraph_filename" />
42fbb6359626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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21 </inputs>
42fbb6359626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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22 <outputs>
42fbb6359626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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23 <data name="output_summary_filename" format="txt"
42fbb6359626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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24 label="${input_sequence_filename} sequence id, median, average, stddev, and seq length" />
42fbb6359626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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25 </outputs>
42fbb6359626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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26 <tests>
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27 <test>
42fbb6359626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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28 <param name="input_sequence_filename" value="test-abund-read-2.fa" />
42fbb6359626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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29 <param name="input_countgraph_filename" value="test-abund-read-2.oxlicg" ftype="oxlicg" />
42fbb6359626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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30 <output name="output_summary_filename">
42fbb6359626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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31 <assert_contents>
42fbb6359626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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32 <has_text text="seq,1001,1001.0,0.0,18" />
42fbb6359626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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33 <has_text text="895:1:37:17593:9954/1,1,21.408163071,141.391921997,114" />
42fbb6359626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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34 </assert_contents>
42fbb6359626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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35 </output>
42fbb6359626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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36 </test>
42fbb6359626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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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,
42fbb6359626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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40 based on the k-mer counts in the given k-mer countgraph. Can be used to
42fbb6359626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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41 estimate expression levels (mRNAseq) or coverage (genomic/metagenomic). The
42fbb6359626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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42 output file contains sequence id, median, average, stddev, and seq length;
42fbb6359626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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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.
42fbb6359626 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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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>