Mercurial > repos > bvalot > fasta_filter_0_1

annotate fastq_subsampling.xml @ 0:bc23da9d464c draft default tip

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planemo upload for repository http://172.20.124.12:3000/bvalot3/PythonScript commit 9676573ee48ce5343600ab45cd3ac1a6adddabe4
author bvalot
date Tue, 14 Jun 2022 08:15:55 +0000
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bc23da9d464c planemo upload for repository http://172.20.124.12:3000/bvalot3/PythonScript commit 9676573ee48ce5343600ab45cd3ac1a6adddabe4
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1 <tool id="fastq_subsampling_wrapper" name="Fastq subsampling" version="0.1">
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2 <description></description>
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3 <requirements>
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4 <requirement type="package" version="0.15">pysam</requirement>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1:" level="fatal" />
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8 </stdio>
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9 <version_command>$__tool_directory__/fastq_subsampling.py -v</version_command>
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10 <command>
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11 $__tool_directory__/fastq_subsampling.py
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12 --galaxy
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13 #if $fastq.choice == "choice1"
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14 -s '${fastq.single}'
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15 #end if
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16 #if $fastq.choice == "choice2"
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17 -r '${fastq.forward}'
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18 -l '${fastq.reverse}'
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19 #end if
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20 #if $fastq.choice == "choice3"
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21 -r '${fastq.pairedfile.forward}'
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22 -l '${fastq.pairedfile.reverse}'
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23 #end if
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24 #if str($coverage)
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25 -c $coverage
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26 #end if
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27 $size
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28 &amp;> '$logfile'
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29 </command>
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30 <inputs>
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31 <conditional name="fastq" >
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32 <param name="choice" type="select" label="Type of reads to subsampling" help="" >
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33 <option value="choice1" selected="true">Single</option>
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34 <option value="choice2">Paired (separated)</option>
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35 <option value="choice3">Paired</option>
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36 </param>
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37 <when value="choice1">
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38 <param name="single" type="data" format="fastq,fastq.gz"
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39 label="Single read file" help="Fastq(gz) format" />
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40 </when>
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41 <when value="choice2">
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42 <param name="forward" type="data" format="fastq,fastq.gz"
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43 label="Forward read file" help="Fastq(gz) format" />
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44 <param name="reverse" type="data" format="fastq,fastq.gz"
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45 label="Reverse read file" help="Fastq(gz) format" />
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46 </when>
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47 <when value="choice3">
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48 <param name="pairedfile" type="data_collection" format="fastq,fastq.gz"
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49 label="Paired of read files" help="Fastq(gz) format"
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50 collection_type="paired" />
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51 </when>
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52 </conditional>
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53 <param name="size" type="integer" optional="false" value="6000000"
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54 label="Size of the genome in bp" />
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55 <param name="coverage" type="integer" value="40" optional="true"
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56 label="Mean coverage to sampling" />
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57 </inputs>
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58
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59 <outputs>
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60 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log" />
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61 <data name="singleout" format="fastqsanger.gz"
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62 label="${tool.name} on ${fastq.single.name}"
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63 from_work_dir="1.fastq.gz">
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64 <filter>fastq['choice'] == "choice1"</filter>
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65 </data>
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66 <data name="forwardout" format="fastqsanger.gz"
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67 label="${tool.name} on ${fastq.forward.name}"
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68 from_work_dir="1.fastq.gz">
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69 <filter>fastq['choice'] == "choice2"</filter>
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70 </data>
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71 <data name="reverseout" format="fastqsanger.gz"
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72 label="${tool.name} on ${fastq.reverse.name}"
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73 from_work_dir="2.fastq.gz">
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74 <filter>fastq['choice'] == "choice2"</filter>
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75 </data>
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76 <collection name="paired_output" type="paired"
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77 label="${tool.name} on ${fastq.pairedfile.name}">
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78 <data name="forward" format="fastqsanger.gz"
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79 from_work_dir="1.fastq.gz">
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80 </data>
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81 <data name="reverse" format="fastqsanger.gz"
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82 from_work_dir="2.fastq.gz">
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83 </data>
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84 <filter>fastq['choice'] == "choice3"</filter>
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85 </collection>
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86 </outputs>
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87 <tests>
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88 <test expect_num_outputs="3">
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89 <param name="choice" value="choice2" />
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90 <param name="forward" value="input_R1.fastq.gz" />
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91 <param name="reverse" value="input_R2.fastq.gz" />
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92 </test>
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93 </tests>
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94 <help>
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95 **What it does**
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96
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97 Subsampling a single or a paired of fastq(.gz) file to a given coverage
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98
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99 **License and citation**
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100
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101 This Galaxy tool is Copyright © 2018 `B. Valot` and is released under the `GPL3 license`.
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102
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103 </help>
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104 <citations>
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105 </citations>
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106 </tool>