Mercurial > repos > iuc > ont_fast5_api_fast5_subset

annotate fast5_subset.xml @ 0:b380520b4420 draft

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"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit 84504d6786e9edf00367739210d6bae78cb42cc8"
author iuc
date Mon, 08 Jun 2020 19:56:06 +0000
parents
children 41bac7dcb43e
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0
b380520b4420 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit 84504d6786e9edf00367739210d6bae78cb42cc8"
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1 <?xml version="1.0"?>
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2 <tool id="ont_fast5_api_fast5_subset" name="Fast5 subset" version="@TOOL_VERSION@+galaxy0" profile="18.01">
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3 <description>of multi read file</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <version_command></version_command>
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9 <command detect_errors="exit_code"><![CDATA[
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10 ## initialize
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11 mkdir data &&
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12 #for $num, $current in enumerate($input):
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13 ln -s '$current' './data/batch${num}.fast5' &&
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14 #end for
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15
b380520b4420 "planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit 84504d6786e9edf00367739210d6bae78cb42cc8"
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16 ## run
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17 fast5_subset
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18 ## required
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19 --input ./data
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20 -s ./results
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21 --read_id_list '$read_id_list'
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22 ## optional
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23 --batch_size $batch_size
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24 -t \${GALAXY_SLOTS:-4}
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25 ]]></command>
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26 <inputs>
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27 <param argument="--input" type="data" format="fast5" multiple="true"
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28 label="Select multi read input file(s)"/>
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29 <param argument="--read_id_list" type="data" format="tabular"
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30 label="Select file with read_ids" help="Either containing 1 read_id per line or a tabular file with a column named read_id."/>
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31 <param argument="--batch_size" type="integer" value="4000" min="1"
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32 label="Set batch size" help="Number of single reads to include in each multi read file"/>
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33 </inputs>
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34 <outputs>
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35 <data name="out_results" format="fast5">
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36 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.fast5" format="fast5" directory="results" assign_primary_output="true" visible="true"/>
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37 </data>
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38 </outputs>
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39 <tests>
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40 <test expect_num_outputs="1">
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41 <param name="input" value="batch.fast5"/>
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42 <param name="read_id_list" value="list.txt"/>
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43 <param name="batch_size" value="2"/>
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44 <output name="out_results">
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45 <assert_contents>
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46 <has_size value="23304"/>
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47 </assert_contents>
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48 <!-- batch0 is represented by out_results -->
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49 <discovered_dataset designation="batch1" ftype="fast5">
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50 <assert_contents>
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51 <has_size value="17328"/>
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52 </assert_contents>
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53 </discovered_dataset>
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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 .. class:: infomark
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59
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60 **What it does**
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61
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62 @WID@
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63
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64 fast5_subset extracts reads from multi_read_fast5_file(s) based on a list of read IDs.
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65
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66 **Input**
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67
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68 A multi read file in FAST5 format and a list of read IDs that should be extracted.
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69
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70 **Output**
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71
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72 A multi read file in FAST5 format containing a subset of the input file.
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73
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74 .. class:: infomark
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75
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76 **References**
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77
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78 @REFERENCES@
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79 ]]></help>
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80 <expand macro="citations"/>
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81 </tool>