annotate ivar_trim.xml @ 2:cb903c9dc33d draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
author iuc
date Wed, 22 Apr 2020 06:05:42 -0400
parents 8858fa037a15
children 5d6ed46cc101
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1 <tool id="ivar_trim" name="ivar trim" version="@VERSION@+galaxy0">
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2 <description>Trim reads in aligned BAM</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="version_command" />
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8 <command detect_errors="exit_code"><![CDATA[
2
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9 #if $primer.source == "history"
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10 ln -s '$primer.input_bed' bed.bed &&
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11 #else
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12 ln -s '$primer.cached_bed.fields.path' bed.bed &&
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13 #end if
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14 ln -s '$input_bam' sorted.bam &&
8858fa037a15 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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15 ivar trim
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16 -i sorted.bam
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17 -b bed.bed
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18 -m $min_len
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19 -q $min_qual
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20 -s $window_width
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21 $inc_primers
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22 -p trimmed &&
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23 samtools sort -@ \${GALAXY_SLOTS:-1} -o trimmed.sorted.bam trimmed.bam &&
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24 samtools index -@ \${GALAXY_SLOTS:-1} trimmed.sorted.bam
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25 ]]> </command>
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26 <inputs>
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27 <param name="input_bam" argument="-i" type="data" format="bam" label="Bam file" help="Aligned reads, to trim primers and quality"/>
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28 <conditional name="primer">
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29 <param label="Source of primer information" name="source" type="select">
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30 <option value="history" selected="true">History</option>
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31 <option value="cached">Built-in</option>
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32 </param>
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33 <when value="history">
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34 <param name="input_bed" argument="-b" type="data" format="bed" label="BED file with primer sequences and positions"/>
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35 </when>
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36 <when value="cached">
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37 <param name="cached_bed" type="select" label="Primer scheme name" help="Select primer scheme bed file from a list">
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38 <options from_data_table="primer_scheme_bedfiles">
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39 <filter type="sort_by" column="1" />
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40 <validator type="no_options" message="No primer schemes are available" />
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41 </options>
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42 </param>
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43 </when>
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44 </conditional>
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45 <param name="min_len" argument="-m" type="integer" min="0" value="30" label="Minimum length of read to retain after trimming"/>
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46 <param name="min_qual" argument="-q" type="integer" min="0" value="20" label="Minimum quality threshold for sliding window to pass"/>
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47 <param name="window_width" argument="-s" type="integer" min="0" value="4" label="Width of sliding window"/>
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48 <param name="inc_primers" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="false" label="Include reads with no primers"/>
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49 </inputs>
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50 <outputs>
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51 <data name="output_bam" format="bam" label="${tool.name} on ${on_string} Trimmed bam" from_work_dir="trimmed.sorted.bam"/>
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52 </outputs>
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53 <tests>
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54 <!-- #1: SARS-Cov data-->
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55 <test>
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56 <param name="input_bam" value="covid19/PC00101P_sub.sorted.bam" />
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57 <param name="input_bed" value="covid19/ARTIC-V1.bed" />
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58 <param name="inc_primers" value="true" />
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59 <output name="output_bam" file="covid19/PC00101P_sub.sorted.bam" compare="sim_size" delta="300000"/>
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60 </test>
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61 <!-- #1: Zika data-->
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62 <test>
2
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63 <conditional name="primer">
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64 <param name="source" value="history" />
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65 <param name="input_bed" value="zika/db/zika_primers.bed" />
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66 </conditional>
0
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67 <param name="input_bam" value="zika/Z52_a.sorted.bam" />
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68 <output name="output_bam" file="zika/Z52_a.trimmed.sorted.bam" compare="sim_size" delta="100000"/>
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69 </test>
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70 <test>
2
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71 <conditional name="primer">
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72 <param name="source" value="history" />
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73 <param name="input_bed" value="zika/db/zika_primers.bed" />
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74 </conditional>
0
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75 <param name="input_bam" value="zika/Z52_b.sorted.bam" />
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76 <output name="output_bam" file="zika/Z52_b.trimmed.sorted.bam" compare="sim_size" delta="100000"/>
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77 </test>
2
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78 <test>
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79 <conditional name="primer">
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80 <param name="source" value="cached" />
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81 <param name="cached_bed" value="SARS-CoV-2-ARTICv1" />
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82 </conditional>
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83 <param name="input_bam" value="sars-cov-2/sars_cov2_untrimmed.bam" ftype="bam" />
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84 <output name="output_bam" file="sars-cov-2/sars_cov2_trimmed.bam" />
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85 </test>
0
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86 </tests>
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87 <help><![CDATA[
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88 iVar uses primer positions supplied in a BED file to soft clip primer
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89 sequences from an aligned and sorted BAM file. Following this, the reads are
8858fa037a15 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd"
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90 trimmed based on a quality threshold(Default: 20). To do the quality
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91 trimming, iVar uses a sliding window approach(Default: 4). The windows
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92 slides from the 5' end to the 3' end and if at any point the average base
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93 quality in the window falls below the threshold, the remaining read is soft
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94 clipped. If after trimming, the length of the read is greater than the
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95 minimum length specified(Default: 30), the read is written to the new
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96 trimmed BAM file
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97
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98 Documentation can be found at `<https://andersen-lab.github.io/ivar/html/manualpage.html>`_.
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99 ]]> </help>
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100 <expand macro="citations" />
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101 </tool>