Mercurial > repos > iuc > khmer_abundance_distribution

annotate abundance-dist.xml @ 0:c07433531fd3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
author iuc
date Wed, 11 Nov 2015 09:46:38 -0500
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children be929aa4e152
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c07433531fd3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
iuc
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1 <tool id="khmer_abundance_distribution" name="Abundance Distribution" version="@WRAPPER_VERSION@.0">
c07433531fd3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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2 <description>
c07433531fd3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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3 Calculate abundance distribution of the k-mers in a given sequence file using a pre-made k-mer countgraph
c07433531fd3 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 <macros>
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6 <token name="@BINARY@">abundance-dist.py</token>
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7 <import>macros.xml</import>
c07433531fd3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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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 &&
c07433531fd3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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14 mkdir output && cd output &&
c07433531fd3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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15 @BINARY@
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16 --squash
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17 ${zero}
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18 ${bigcount}
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19 ${input_countgraph_filename}
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20 ${input_sequence_filename}
c07433531fd3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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21 ${output_histogram_filename}
c07433531fd3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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22 ]]>
c07433531fd3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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23 </command>
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24 <inputs>
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25 <expand macro="input_countgraph_filename" />
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26 <expand macro="input_sequence_filename" />
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27 <expand macro="input_zero" />
c07433531fd3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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28 <expand macro="input_bigcount" />
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29 </inputs>
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30 <outputs>
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31 <expand macro="abundance-histogram-output" />
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32 </outputs>
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33 <tests>
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34 <test>
c07433531fd3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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35 <param name="input_sequence_filename" value="test-abund-read-2.fa" />
c07433531fd3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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36 <param name="input_countgraph_filename" value="test-abund-read-2.oxlicg" ftype="oxlicg" />
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37 <param name="zero" value="false" />
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38 <output name="output_histogram_filename">
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39 <assert_contents>
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40 <has_text text="1,96,96,0.98" />
c07433531fd3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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41 <has_text text="1001,2,98,1.0" />
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42 </assert_contents>
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43 </output>
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44 </test>
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45 <test>
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46 <param name="input_sequence_filename" value="test-abund-read-2.fa" />
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47 <param name="input_countgraph_filename" value="test-abund-read-2.oxlicg" ftype="oxlicg" />
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48 <param name="zero" value="false" />
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49 <param name="bigcount" value="false" />
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50 <output name="output_histogram_filename">
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51 <assert_contents>
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52 <has_text text="1,96,96,0.98" />
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53 <has_text text="255,2,98,1.0" />
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54 </assert_contents>
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55 </output>
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56 </test>
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57 </tests>
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58 <help><![CDATA[
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59 Calculate abundance distribution of the k-mers in the sequence file using a
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60 pre-made k-mer countgraph.
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61
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62 @HELP_FOOTER@
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63 ]]>
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64 </help>
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65 <citations>
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66 <expand macro="software-citation" />
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67 <expand macro="counting-citation" />
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68 </citations>
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69 </tool>