Mercurial > repos > iuc > khmer_extract_partitions

annotate extract-partitions.xml @ 9:1061711538c6 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 238d0992c63de53623c4fc05eec8bd8d67001997
author iuc
date Thu, 03 Oct 2024 13:46:53 +0000
parents adb3dd5a899f
children
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98b53d46e851 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 14ea2dc5ef36219c908ed64b256794711ce7b902"
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1 <tool id="khmer_extract_partitions" name="khmer: Extract partitions" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>Separate sequences that are annotated with partitions into grouped files</description>
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3 <macros>
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4 <token name="@BINARY@">extract-partitions.py</token>
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5 <import>macros.xml</import>
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6 </macros>
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1061711538c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 238d0992c63de53623c4fc05eec8bd8d67001997
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7 <expand macro="bio_tools"/>
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8 <expand macro="requirements" />
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9 <expand macro="stdio" />
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10 <expand macro="version" />
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11 <command><![CDATA[
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12 mkdir -p output &&
d5a18dd63529 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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13 cd output &&
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14 @BINARY@
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15 --max-size $max_size
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16 --min-partition-size $min_partition_size
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17 $output_unassigned
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18 output
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19 #for input in $inputs
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20 $input
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21 #end for
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22 ]]>
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23 </command>
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24 <inputs>
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25 <expand macro="input_sequences_filenames" />
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26 <param argument="--max-size" type="integer" label="Max group size" value="1000000"
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27 help="No more than this many number of sequences will be stored in each output"/>
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28 <param name="min_partition_size" type="integer" label="Min partition size" value="5"
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29 help="The minimum partition size worth keeping (--min-partition-size/-m)" />
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30 <param name="output_unassigned" type="boolean" checked="false" truevalue="--output-unassigned" falsevalue=""
d5a18dd63529 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2
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31 label="Output unassigned sequences" help="(--output-unassigned/-U)" />
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32 </inputs>
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33 <outputs>
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34 <data name="distribution" format="txt" from_work_dir="output/output.dist" label="${tool.name} on ${on_string}: Partition size distribution" />
1061711538c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 238d0992c63de53623c4fc05eec8bd8d67001997
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35 <collection name="groups_of_partitions" type="list" format="fasta">
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36 <discover_datasets pattern="__name__" directory="output" format="fasta"/>
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37 </collection>
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38 </outputs>
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39 <tests>
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40 <test>
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41 <param name="inputs" value="random-20-a.fa.part"/>
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42 <output name="distribution">
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43 <assert_contents>
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44 <has_text text="99 1 1 99"/>
1061711538c6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer commit 238d0992c63de53623c4fc05eec8bd8d67001997
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45 </assert_contents>
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46 </output>
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47 <output_collection name="groups_of_partitions">
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48 <element name="output.group0000.fa" file="random-20-a.part.extract.fa" />
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49 </output_collection>
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50 </test>
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51
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52 </tests>
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53 <help><![CDATA[
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54 Separate sequences that are annotated with partitions into grouped files.
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55
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56 @HELP_FOOTER@
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57 ]]>
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58 </help>
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59 <citations>
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60 <expand macro="software-citation" />
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61 <expand macro="graph-citation" />
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62 </citations>
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63 </tool>