Mercurial > repos > jvolkening > b2b_summarize_run

annotate summarize_run.xml @ 1:b31b119e3905 draft default tip

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
author jvolkening
date Fri, 08 Mar 2024 00:44:15 +0000
parents 9e0453df1745
children
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1 <tool id="b2b_summarize_run" name="Summarize run" version="0.002">
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3 <description>Summarize sequencing run and assembly statistics</description>
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5 <!-- ***************************************************************** -->
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7 <requirements>
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8 <!--
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9 <requirement type="package" version="0.003">b2b-utils</requirement>
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10 -->
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11 <requirement type="package" version="0.7.17">bwa</requirement>
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12 <requirement type="package" version="0.008009">perl-biox-seq</requirement>
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13 <requirement type="package" version="1.23">perl-file-which</requirement>
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14 </requirements>
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16 <!-- ***************************************************************** -->
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18 <version_command>echo "0.002"</version_command>
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20 <!-- ***************************************************************** -->
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22 <command detect_errors="aggressive">
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23 <![CDATA[
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24 perl $__tool_directory__/frag_lens
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25 --forward "$in_filt1"
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26 --reverse "$in_filt2"
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27 --ref "$in_ref"
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28 --threads "\${GALAXY_SLOTS:-1}"
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29 --max_aln 100000
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30 | perl $__tool_directory__/summarize_run.pl
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31 --raw_1 $in_raw1
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32 --raw_2 $in_raw2
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33 --filt_1 $in_filt1
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34 --filt_2 $in_filt2
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35 --consensus $in_ref
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36 --bedgraph $in_bg
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37 --fastqc_1 $in_fqc1
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38 --fastqc_2 $in_fqc2
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39 --out $report
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40 --threads "\${GALAXY_SLOTS:-1}"
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41 ;
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42
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43 ]]>
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44 </command>
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46 <!-- ***************************************************************** -->
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48 <inputs>
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49 <param format="fastqsanger,fastq" name="in_raw1" type="data" label="Raw forward reads" />
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50 <param format="fastqsanger,fastq" name="in_raw2" type="data" label="Raw reverse reads" />
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51 <param format="fastqsanger,fastq" name="in_filt1" type="data" label="Filtered/synced forward reads" />
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52 <param format="fastqsanger,fastq" name="in_filt2" type="data" label="Filtered/synced reverse reads" />
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53 <param format="fasta" name="in_ref" type="data" label="Consensus (FASTA)" />
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54 <param format="bedgraph" name="in_bg" type="data" label="Coverage (bedgraph)" />
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55 <param format="txt" name="in_fqc1" type="data" label="Raw FastQC (forward reads)" />
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56 <param format="txt" name="in_fqc2" type="data" label="Raw FastQC (reverse reads)" />
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57 </inputs>
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58
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59 <!-- ***************************************************************** -->
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61 <outputs>
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62 <data format="tabular" name="report" label="Run/assembly summary" />
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63 </outputs>
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65 <!-- ***************************************************************** -->
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67 <tests>
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68 <test>
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69 <param name="in_raw1" value="sumrun_R1.fq" ftype="fastq" />
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70 <param name="in_raw2" value="sumrun_R2.fq" ftype="fastq" />
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71 <param name="in_filt1" value="sumrun_sync_R1.fq" ftype="fastq" />
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72 <param name="in_filt2" value="sumrun_sync_R2.fq" ftype="fastq" />
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73 <param name="in_ref" value="sumrun_ref.fa" ftype="fasta" />
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74 <param name="in_bg" value="sumrun_ref.bg" ftype="bedgraph" />
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75 <param name="in_fqc1" value="sumrun_R1.fastqc" ftype="txt" />
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76 <param name="in_fqc2" value="sumrun_R2.fastqc" ftype="txt" />
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77 <output name="report" file="sumrun.report.tsv" compare="diff" />
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78 </test>
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79 </tests>
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80
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81 <!-- ***************************************************************** -->
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82
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83 <help>
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85 `summarize_run` is a Galaxy-only utility from BASE2BIO that reports a
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86 number of summary statistics for a sequencing run and assembly. It was
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87 written to support workflows at the USDA Southeast Poultry Research
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88 Laboratory and may be of limited general-purpose application.
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90 </help>
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92 <!-- ***************************************************************** -->
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94 <citations>
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95 </citations>
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97 </tool>
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98