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annotate do-partition.xml @ 60:fe697e0cb24a draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit d8e0950d53e504e02ee5db43c0804142b14d7fd2-dirty
author crusoe
date Tue, 07 Jul 2015 11:59:39 -0400
parents 08a599cf71d0
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1 <tool id="gedlab-khmer-do-partition"
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2 name="Sequence partition all-in-one"
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3 version="2.0rc1-1">
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4
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5 <description>
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6 Load, partition, and annotate FAST[AQ] sequences
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7 </description>
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8 <macros>
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9 <token name="@BINARY@">do-parition.py</token>
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10 <import>macros.xml</import>
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11 </macros>
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12 <expand macro="requirements" />
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13 <expand macro="stdio" />
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14 <expand macro="version" />
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15 <command><![CDATA[
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16 mkdir -p output;
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17 @BINARY@
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18 @TABLEPARAMS@
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19 @THREADS@
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20 output
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21 #for input in $inputs
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22 $input
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23 #end for ;
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24 mv output.info $infomation ;
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25 mv *.part output/
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26 ]]>
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27 </command>
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28
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29 <inputs>
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30 <expand macro="input_sequences_filenames" />
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31 <param name="ksize"
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32 type="integer"
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33 value="20"
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34 label="ksize"
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35 help="k-mer size to use (--ksize/-k)" />
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36 <param name="n_tables"
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37 type="integer"
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38 min="1"
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39 value="4"
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40 label="n_tables"
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41 help="number of tables to use (--n_tables/-N)" />
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42 <param name="tablesize_specific"
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43 type="text"
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44 label="tablesize"
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45 help="lower bound on the tablesize to use (--min-tablesize/-x)" />
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46 </inputs>
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47 <outputs>
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48 <data name="information"
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49 format="text"
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50 label="${tool.name} summary for #echo ','.join(map(str, $inputs ))#" />
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51 <expand macro="output_sequences" />
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52 </outputs>
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53 <tests>
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54 <test>
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55 <param name="inputs" value="random-20-a.fa"/>
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56 <output name="output">
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57 <discovered_dataset designation="random-20-a.fa.part">
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58 <assert_contents>
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59 <has_text text='>35 2' />
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60 </assert_contents>
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61 </discovered_dataset>
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62 </output>
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63 </test>
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64 </tests>
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65 <help><![CDATA[
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66 Load in a set of sequences, partition them, merge the partitions, and
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67 annotate the original sequences files with the partition information.
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69 This script combines the functionality of :program:`load-graph.py`,
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70 :program:`partition-graph.py`, :program:`merge-partitions.py`, and
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71 :program:`annotate-partitions.py` into one script. This is convenient
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72 but should probably not be used for large data sets, because
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73 :program:`do-partition.py` doesn't provide save/resume functionality.
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74 ]]>
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75 </help>
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76 <citations>
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77 <expand macro="software-citation" />
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78 <expand macro="graph-citation" />
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79 </citations>
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80 </tool>