annotate abundance-dist.xml @ 7:e0de12ae3fc2 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
author iuc
date Wed, 18 Dec 2019 15:59:06 -0500
parents be929aa4e152
children c0caca5af183
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e0de12ae3fc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
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1 <tool id="khmer_abundance_distribution" name="khmer: Abundance Distribution" version="@WRAPPER_VERSION@@TOOL_VERSION@">
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2 <description>
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3 Calculate abundance distribution of k-mers using pre-made k-mer countgraphs
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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>
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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[
7
e0de12ae3fc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 7de685f4763d988a5a9abce4a9c2b4714daaf165"
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13 set -u &&
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14 @BINARY@
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15 --squash
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16 ${zero}
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17 ${bigcount}
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18 ${input_countgraph_filename}
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19 ${input_sequence_filename}
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20 ${output_histogram_filename}
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21 ]]>
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22 </command>
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23 <inputs>
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24 <expand macro="input_countgraph_filename" />
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25 <expand macro="input_sequence_filename" />
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26 <expand macro="input_zero" />
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27 <expand macro="input_bigcount" />
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28 </inputs>
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29 <outputs>
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30 <expand macro="abundance-histogram-output" />
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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="input_sequence_filename" value="test-abund-read-2.fa" />
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35 <param name="input_countgraph_filename" value="test-abund-read-2.oxlicg" ftype="oxlicg" />
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36 <param name="zero" value="false" />
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37 <output name="output_histogram_filename">
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38 <assert_contents>
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39 <has_text text="1,96,96,0.98" />
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40 <has_text text="1001,2,98,1.0" />
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41 </assert_contents>
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42 </output>
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43 </test>
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44 <test>
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45 <param name="input_sequence_filename" value="test-abund-read-2.fa.gz" />
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46 <param name="input_countgraph_filename" value="test-abund-read-2.oxlicg" ftype="oxlicg" />
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47 <param name="zero" value="false" />
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48 <param name="bigcount" value="false" />
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49 <output name="output_histogram_filename">
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50 <assert_contents>
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51 <has_text text="1,96,96,0.98" />
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52 <has_text text="255,2,98,1.0" />
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53 </assert_contents>
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54 </output>
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55 </test>
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56 </tests>
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57 <help><![CDATA[
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58 Calculate abundance distribution of the k-mers in the sequence file using a
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59 pre-made k-mer countgraph.
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60
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61 @HELP_FOOTER@
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62 ]]>
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63 </help>
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64 <citations>
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65 <expand macro="software-citation" />
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66 <expand macro="counting-citation" />
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67 </citations>
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68 </tool>