Mercurial > repos > nml > fastqc_stats

annotate fastqc_stats.xml @ 0:2c74c5c70520 draft default tip

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planemo upload for repository https://github.com/phac-nml/galaxy_tools commit d5b7cb71616c0ac20e02ff8cb8c147b9d4a31691
author nml
date Wed, 11 Oct 2017 16:22:08 -0400
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1 <tool id="FastQC_Summary" name="FastQC Summary" version="1.2">
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2 <description>Provide a one line summary of a FastQC report(s)</description>
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3 <requirements>
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4 <requirement type="package" version="1.6.924">perl-bioperl</requirement>
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5 <requirement type="package" version="2.49">perl-getopt-long</requirement>
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6 </requirements>
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7 <command detect_errors="exit_code"><![CDATA[
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8
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9 perl $__tool_directory__/fastqc_stats.pl
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12 #if $single_or_mate.library_type == "single"
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13 --fastq_se $single_or_mate.fastq_file --g_rawdata_se $rawdata_file
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14 --sample "$single_or_mate.fastq_file.name"
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15 #elif $single_or_mate.library_type == "paired"
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16 --fastq_pe_1 $single_or_mate.forward_fastq --fastq_pe_2 $single_or_mate.reverse_fastq --g_rawdata_pe_1 $single_or_mate.forward_rawdata --g_rawdata_pe_2 $single_or_mate.reverse_rawdata
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17 --sample "$single_or_mate.forward_fastq.name"
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18 #else
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19 --fastq_pe_1 $single_or_mate.fastq_collection.forward --fastq_pe_2 $single_or_mate.fastq_collection.reverse --g_rawdata_pe_1 $single_or_mate.fastqc_collection.forward --g_rawdata_pe_2 $single_or_mate.fastqc_collection.reverse
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20 --sample "$single_or_mate.fastq_collection.name"
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21 #end if
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24
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25 #if $ref_or_num.select == "reference"
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26 --ref $ref_or_num.ref_file
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27 #else
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28 --num_bps $ref_or_num.bp_num
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29 #end if
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30 -o $out_file
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31
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32 ]]></command>
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33 <inputs>
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34 <conditional name="single_or_mate">
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35 <param name="library_type" type="select" label="Is this library single or paired-end?">
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36 <option value="single">Single-end</option>
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37 <option value="paired">Paired-end</option>
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38 <option value="collection">Collection Paired-end Fastqs</option>
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39 </param>
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40 <when value="single">
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41 <param name="fastq_file" type="data" format="fastqsanger,fastq" label="Single end FASTQ"/>
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42 <param name="rawdata_file" type="data" format="txt" label="FastQC RawData"/>
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43 </when>
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44 <when value="paired">
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45 <param name="forward_fastq" type="data" format="fastqsanger,fastq" label="Forward FASTQ"/>
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46 <param name="reverse_fastq" type="data" format="fastqsanger,fastq" label="Reverse FASTQ"/>
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47 <param name="forward_rawdata" type="data" format="txt" label="FASTQC forward RawData"/>
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48 <param name="reverse_rawdata" type="data" format="txt" label="FASTQC reverse RawData"/>
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49 </when>
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50 <when value="collection">
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51 <param name="fastq_collection" type="data_collection" label="Paired-end Fastq collection" help="" optional="false" format="txt" collection_type="paired" />
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52 <param name="fastqc_collection" type="data_collection" label="Paired-end FastQC collection" help="" optional="false" format="txt" collection_type="paired" />
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53 </when>
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54 </conditional>
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55 <conditional name="ref_or_num">
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56 <param name="select" type="select" label="Reference file or number of base pairs?">
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57 <option value="reference">Reference file</option>
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58 <option value="num_pairs">Number of base pairs</option>
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59 </param>
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60 <when value="reference">
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61 <param name="ref_file" type="data" format='fasta' help="To determine raw genome coverage." label="Reference file"/>
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62 </when>
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63 <when value="num_pairs">
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64 <param name="bp_num" type="integer" value="" label="Number of base pairs"/>
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65 </when>
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66 </conditional>
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67 </inputs>
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68 <outputs>
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69 <data format="tabular" name="out_file" label="Output csv file"/>
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70 </outputs>
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71 <tests>
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72 <test>
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73 <param name="fastq_file" value="forward.fastq"/>
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74 <param name="rawdata_file" value="forward.txt"/>
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75 <param name="ref_file" value="reference_1K.fa"/>
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76 <output name="out_file" value="output_single.tsv"/>
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77 </test>
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78 <test>
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79 <param name="library_type" value="paired"/>
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80 <param name="forward_fastq" value="forward.fastq"/>
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81 <param name="reverse_fastq" value="reverse.fastq"/>
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82 <param name="forward_rawdata" value="forward.txt"/>
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83 <param name="reverse_rawdata" value="reverse.txt"/>
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84 <param name="ref_file" value="reference_1K.fa"/>
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85 <output name="out_file" value="output_pe.tsv"/>
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86 </test>
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87 </tests>
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88 <help>
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89
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90 What it does
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91 ============
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92 This script provides a one line summary of the FastQC report.
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93
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94 Inputs
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95 ======
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96 - **Is this library single or paired end?**: Choose Single-end or Paired-end. This option will display the correct number of input fields depending on the option selected
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97 - **Fastq input**: - Fastqc file
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98 - **FastQC rawData input**: - This is the txt file produced by the FastQC tool
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99 - **Sample Name**: Sample name that will appear in the output file
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100 - **Reference file or number of base pairs?**: Choose between providing a reference file or providing a number of basepairs to determine the raw genome coverage.
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101
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102 Outputs
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103 =======
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104 - **Output csv file**: Summarizes the FastQC report in a csv format
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105 </help>
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106 </tool>