Mercurial > repos > iuc > khmer_abundance_distribution_single

annotate abundance-dist-single.xml @ 0:47cea67b74ea 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 09:47:17 -0500
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children a3a5a1e44d18
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47cea67b74ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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1 <tool id="khmer_abundance_distribution_single" name="Abundance Distribution (all-in-one)" version="@WRAPPER_VERSION@.0">
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2 <description>
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3 Calculate abundance distribution of the k-mers in a given sequence file
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4 </description>
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5 <macros>
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6 <token name="@BINARY@">abundance-dist-single.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[
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13 set -xu &&
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14 mkdir output && cd output &&
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15 @BINARY@
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16 @TABLEPARAMS@
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17 ${zero}
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18 ${bigcount}
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19 #if $save_countgraph
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20 --savegraph=${optional_output_countgraph}
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21 #end if
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22 --squash
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23 @THREADS@
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24 ${input_sequence_filename}
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25 ${output_histogram_filename}
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26
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27 ]]>
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28 </command>
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29 <inputs>
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30 <expand macro="input_sequence_filename" />
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31 <param name="save_countgraph" type="boolean" label="Save the k-mer countgraph to a file"
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32 help="(--savegraph)" />
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33 <expand macro="input_zero" />
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34 <expand macro="input_bigcount" />
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35 <expand macro="tableinputs" />
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36 </inputs>
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37 <outputs>
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38 <data name="optional_output_countgraph" format="oxlicg" label="${tool.name} k-mer countgraph">
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39 <filter>save_countgraph == True</filter>
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40 </data>
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41 <expand macro="abundance-histogram-output" />
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42 </outputs>
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43 <tests>
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44 <test>
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45 <param name="input_sequence_filename" value="test-abund-read-2.fa" />
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46 <param name="type" value="specific" />
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47 <param name="tablesize_specific" value="1e7" />
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48 <param name="n_tables" value="2" />
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49 <param name="ksize" value="17" />
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50 <param name="no_zero" value="false" />
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51 <output name="output_histogram_filename" ftpye="txt">
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52 <assert_contents>
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53 <has_text text="1,96,96,0.98" />
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54 <has_text text="1001,2,98,1.0" />
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55 </assert_contents>
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56 </output>
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57 </test>
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58 <test>
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59 <param name="input_sequence_filename" value="test-abund-read-2.fa" />
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60 <param name="type" value="specific" />
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61 <param name="tablesize_specific" value="1e7" />
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62 <param name="n_tables" value="2" />
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63 <param name="ksize" value="17" />
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64 <param name="no_zero" value="false" />
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65 <param name="bigcount" value="false" />
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66 <output name="output_histogram_filename" ftype="txt">
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67 <assert_contents>
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68 <has_text text="1,96,96,0.98" />
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69 <has_text text="255,2,98,1.0" />
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70 </assert_contents>
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71 </output>
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72 </test>
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73
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74 </tests>
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75 <help><![CDATA[
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76 Calculate the abundance distribution of k-mers from a single sequence file.
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77
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78 Note that with `-b` this script is constant memory; in exchange,
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79 k-mer counts will stop at 255. The memory usage of this script with
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80 `-b` will be about 1.15x the product of the `-x` and
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81 `-N` numbers.
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82
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83
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84 @HELP_FOOTER@
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85 ]]>
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86 </help>
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87 <citations>
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88 <expand macro="software-citation" />
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89 <expand macro="counting-citation" />
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90 </citations>
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91 </tool>