Mercurial > repos > thanhlv > bbmap

annotate filter_by_name.xml @ 5:5127e62d11fb draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit f832310ee25935e283f72f057790af7fad0d661b-dirty"
author thanhlv
date Wed, 18 Mar 2020 21:24:20 +0000
parents e40d2adb0896
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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e40d2adb0896 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit d468e81e47906b2427e4e61f70101fac00a34aab-dirty"
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1 <?xml version="1.0"?>
e40d2adb0896 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit d468e81e47906b2427e4e61f70101fac00a34aab-dirty"
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2 <tool id="bbmap_filterbyname" name="filter_by_name" version="@VERSION@">
e40d2adb0896 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit d468e81e47906b2427e4e61f70101fac00a34aab-dirty"
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3 <description>Filters reads by name</description>
e40d2adb0896 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit d468e81e47906b2427e4e61f70101fac00a34aab-dirty"
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4 <macros>
e40d2adb0896 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit d468e81e47906b2427e4e61f70101fac00a34aab-dirty"
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5 <import>macros.xml</import>
e40d2adb0896 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit d468e81e47906b2427e4e61f70101fac00a34aab-dirty"
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6 </macros>
e40d2adb0896 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit d468e81e47906b2427e4e61f70101fac00a34aab-dirty"
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7 <expand macro="requirements" />
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8 <expand macro="version_command" />
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9
e40d2adb0896 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit d468e81e47906b2427e4e61f70101fac00a34aab-dirty"
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10 <command><![CDATA[
e40d2adb0896 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit d468e81e47906b2427e4e61f70101fac00a34aab-dirty"
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11 #if $singlePaired.sPaired == "single":
e40d2adb0896 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit d468e81e47906b2427e4e61f70101fac00a34aab-dirty"
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12 #if $singlePaired.input_singles.is_of_type("fastq.gz"):
e40d2adb0896 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit d468e81e47906b2427e4e61f70101fac00a34aab-dirty"
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13 #set read1 = 'input_1.fastq.gz'
e40d2adb0896 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit d468e81e47906b2427e4e61f70101fac00a34aab-dirty"
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14 #set compressed = 'gz'
e40d2adb0896 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit d468e81e47906b2427e4e61f70101fac00a34aab-dirty"
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15 #else
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16 #set read1 = 'input_1.fastq'
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17 #end if
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e40d2adb0896 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit d468e81e47906b2427e4e61f70101fac00a34aab-dirty"
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19 #set fil_input = 'in='+ $read1 + ' out=f_read.fq'
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21 ln -s '${singlePaired.input_singles}' ${read1} &&
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22 #elif $singlePaired.sPaired == "paired":
e40d2adb0896 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit d468e81e47906b2427e4e61f70101fac00a34aab-dirty"
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23 #if $singlePaired.input_mate1.is_of_type("fastq.gz"):
e40d2adb0896 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit d468e81e47906b2427e4e61f70101fac00a34aab-dirty"
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24 #set read1 = 'input_1.fastq.gz'
e40d2adb0896 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit d468e81e47906b2427e4e61f70101fac00a34aab-dirty"
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25 #set compressed = 'gz'
e40d2adb0896 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit d468e81e47906b2427e4e61f70101fac00a34aab-dirty"
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26 #else
e40d2adb0896 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit d468e81e47906b2427e4e61f70101fac00a34aab-dirty"
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27 #set read1 = 'input_1.fastq'
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28 #end if
e40d2adb0896 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit d468e81e47906b2427e4e61f70101fac00a34aab-dirty"
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29
e40d2adb0896 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit d468e81e47906b2427e4e61f70101fac00a34aab-dirty"
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30 ln -s '${singlePaired.input_mate1}' ${read1} &&
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31
e40d2adb0896 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit d468e81e47906b2427e4e61f70101fac00a34aab-dirty"
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32 #if $singlePaired.input_mate2.is_of_type("fastq.gz"):
e40d2adb0896 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit d468e81e47906b2427e4e61f70101fac00a34aab-dirty"
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33 #set read2 = 'input_2.fastq.gz'
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34 #else
e40d2adb0896 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit d468e81e47906b2427e4e61f70101fac00a34aab-dirty"
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35 #set read2 = 'input_2.fastq'
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36 #end if
e40d2adb0896 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit d468e81e47906b2427e4e61f70101fac00a34aab-dirty"
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37 ln -s '${singlePaired.input_mate2}' ${read2} &&
e40d2adb0896 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit d468e81e47906b2427e4e61f70101fac00a34aab-dirty"
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38 #set fil_input = 'in=' + $read1 + ' in2=' + $read2 + ' out=f_read1.fq out2=f_read2.fq'
e40d2adb0896 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit d468e81e47906b2427e4e61f70101fac00a34aab-dirty"
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39 #else:
e40d2adb0896 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit d468e81e47906b2427e4e61f70101fac00a34aab-dirty"
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40 #if $singlePaired.input_mate_pairs.forward.is_of_type("fastq.gz"):
e40d2adb0896 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit d468e81e47906b2427e4e61f70101fac00a34aab-dirty"
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41 #set read1 = 'input_1.fastq.gz'
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42 #set compressed = 'gz'
e40d2adb0896 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit d468e81e47906b2427e4e61f70101fac00a34aab-dirty"
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43 #else
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44 #set read1 = 'input_1.fastq'
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45 #end if
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46 ln -s '${singlePaired.input_mate_pairs.forward}' ${read1} &&
e40d2adb0896 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit d468e81e47906b2427e4e61f70101fac00a34aab-dirty"
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47
e40d2adb0896 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit d468e81e47906b2427e4e61f70101fac00a34aab-dirty"
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48 #if $singlePaired.input_mate_pairs.reverse.is_of_type("fastq.gz"):
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49 #set read2 = 'input_2.fastq.gz'
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50 #else
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51 #set read2 = 'input_2.fastq'
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52 #end if
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53 ln -s '${singlePaired.input_mate_pairs.reverse}' ${read2} &&
e40d2adb0896 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit d468e81e47906b2427e4e61f70101fac00a34aab-dirty"
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54 #set fil_input = 'in=' + $read1 + ' in2=' + $read2 + ' out=f_read1.fq out2=f_read2.fq'
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55 #end if
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56
e40d2adb0896 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit d468e81e47906b2427e4e61f70101fac00a34aab-dirty"
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57 filterbyname.sh
e40d2adb0896 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit d468e81e47906b2427e4e61f70101fac00a34aab-dirty"
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58 ${fil_input}
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59 #if $source.type == "input_string":
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60 names=$source.in_string
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61 #elif $source.type == "name":
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62 names=$source.name_list
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63 #end if
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64 include=$include
5
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65 #if $q33
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66 qin=33
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67 #end if
4
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68 2>&1 | tee > log.txt
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69 ]]> </command>
e40d2adb0896 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit d468e81e47906b2427e4e61f70101fac00a34aab-dirty"
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70 <inputs>
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71 <conditional name="singlePaired">
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72 <param name="sPaired" type="select" label="Is the input paired- or single-end?">
e40d2adb0896 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit d468e81e47906b2427e4e61f70101fac00a34aab-dirty"
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73 <option value="single">Single-end</option>
e40d2adb0896 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit d468e81e47906b2427e4e61f70101fac00a34aab-dirty"
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74 <option value="paired">Paired-end</option>
e40d2adb0896 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit d468e81e47906b2427e4e61f70101fac00a34aab-dirty"
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75 <option value="paired_collection">Paired Collection</option>
e40d2adb0896 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit d468e81e47906b2427e4e61f70101fac00a34aab-dirty"
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76 </param>
e40d2adb0896 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit d468e81e47906b2427e4e61f70101fac00a34aab-dirty"
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77 <when value="single">
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78 <param name="input_singles" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" label="Reads in FASTQ format" />
e40d2adb0896 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit d468e81e47906b2427e4e61f70101fac00a34aab-dirty"
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79 </when>
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80 <when value="paired">
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81 <param name="input_mate1" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" label="Forward read" />
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82 <param name="input_mate2" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" label="Reversed read" />
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83 </when>
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84 <when value="paired_collection">
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85 <param name="input_mate_pairs" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
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86 </when>
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87 </conditional>
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88 <conditional name="source">
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89 <param name="type" type="select" label="Select source of sequence choices">
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90 <option value="input_string">Text</option>
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91 <option value="name">FASTA/Q ID list</option>
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92 </param>
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93 <when value="input_string">
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94 <param name="in_string" type="text" label="Input string" help="string1,string2,string3,...,stringn"/>
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95 </when>
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96 <when value="name">
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97 <param name="name_list" type="data" format="txt" label="Input ID list"/>
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98 </when>
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99 </conditional>
5
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100 <param name="q33" type="boolean" truevalue="true" falsevalue="" checked="false" label="Q33?" />
4
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101 <param name="include" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Include the filtered names" />
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102 </inputs>
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103 <outputs>
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104 <data name="log" from_work_dir="log.txt" format="txt" label="${tool.name} on ${on_string}: Log" />
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105 <data format_source="input_singles" name="filtered_reads_single" from_work_dir="f_read.fq" label="${tool.name} on ${on_string}: filtered reads">
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106 <filter>singlePaired['sPaired'] == "single"</filter>
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107 </data>
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108 <data format="fastqsanger" name="filtered_reads_pair1" from_work_dir="f_read1.fq" label="${tool.name} on ${on_string}: filtered reads pair 1">
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109 <filter>singlePaired['sPaired'] == "paired"</filter>
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110 </data>
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111
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112 <data format="fastqsanger" name="filtered_reads_pair2" from_work_dir="f_read2.fq" label="${tool.name} on ${on_string}: filtered reads pair 2">
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113 <filter>singlePaired['sPaired'] == "paired"</filter>
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114 </data>
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115
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116 <collection name="filtered_collection" type="paired" label="${tool.name} on ${on_string}: Filtered reads by name">
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117 <data name="forward" format_source="input_mate_pairs['forward']" from_work_dir="f_read1.fq"/>
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118 <data name="reverse" format_source="input_mate_pairs['forward']" from_work_dir="f_read2.fq"/>
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119 <filter>singlePaired['sPaired'] == "paired_collection"</filter>
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120 </collection>
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121 </outputs>
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122 <tests>
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123 <test>
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124 <param name="sPaired" value="paired"/>
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125 <param name="input_mate1" value="forward.fq.gz"/>
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126 <param name="input_mate1" value="reverse.fq.gz"/>
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127 <param name="type" value="name"/>
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128 <param name="name_list" value="name.list"/>
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129 <output name="filtered_reads_pair1" value="f_read1.fq" ftype="fastqsanger" compare="sim_size"/>
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130 <output name="filtered_reads_pair2" value="f_read2.fq" ftype="fastqsanger" compare="sim_size"/>
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131 </test>
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132 </tests>
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133 <help><![CDATA[
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134 ]]> </help>
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135 <expand macro="citations" />
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136 </tool>