Mercurial > repos > jdv > b2b_sync_reads

annotate sync_reads.xml @ 0:6466424fc8ac draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
author jdv
date Wed, 17 Jul 2019 17:48:50 -0400
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children b7f66945bf72
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6466424fc8ac planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
jdv
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1 <tool id="b2b_sync_reads" name="Sync paired reads" version="0.004">
6466424fc8ac planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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3 <description>Synchronize trimmed/filtered read-pair set</description>
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5 <!-- ***************************************************************** -->
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7 <requirements>
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8 <!-- <requirement type="package" version="0.003">b2b-utils</requirement> -->
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9 <requirement type="package" version="0.006007">perl-biox-seq</requirement>
6466424fc8ac planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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10 </requirements>
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6466424fc8ac planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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12 <!-- ***************************************************************** -->
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6466424fc8ac planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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14 <version_command>sync_reads --version | perl -wnE'print "$1\n" for /sync_reads v(.+)/g'</version_command>
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6466424fc8ac planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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16 <!-- ***************************************************************** -->
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18 <command detect_errors="aggressive">
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19 <![CDATA[
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21 sync_reads
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22 --fwd $input1
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23 --rev $input2
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24 --fwd_out $fwd_out
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25 --rev_out $rev_out
6466424fc8ac planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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26 #if str($write_singles) == 'y':
6466424fc8ac planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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27 --singles
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28 --fwd_singles_out $fwd_s_out
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29 --rev_singles_out $rev_s_out
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30 #end if
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32 ]]>
6466424fc8ac planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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33 </command>
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6466424fc8ac planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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35 <!-- ***************************************************************** -->
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37 <inputs>
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6466424fc8ac planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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39 <param name="job_name" type="text" size="120" value="sync_reads" label="Job narrative (added to output names)"
6466424fc8ac planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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40 help="Only letters, numbers and underscores (_) will be retained in this field">
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41 <sanitizer invalid_char="">
6466424fc8ac planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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42 <valid initial="string.letters,string.digits"><add value="_" /> </valid>
6466424fc8ac planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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43 </sanitizer>
6466424fc8ac planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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44 </param>
6466424fc8ac planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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45 <!-- FASTQ input(s) and options specifically for paired-end data. -->
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46 <param name="input1" format="fastqsanger,fastq" type="data" label="Forward read FASTQ file" help="Forward read FASTQ file"/>
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47 <param name="input2" format="fastqsanger,fastq" type="data" label="Reverse read FASTQ file" help="Reverse read FASTQ file"/>
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48 <param name="write_singles" type="boolean" label="Output singletons" checked="False" truevalue="y" falsevalue="n" />
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49
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50 </inputs>
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6466424fc8ac planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit b5d52d0664b01d252cf61b98be373d09f1ecc2df
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52 <!-- ***************************************************************** -->
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54 <outputs>
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55 <data format_source="input1" name="fwd_out" label="${job_name}_sync.1.fq" />
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56 <data format_source="input2" name="rev_out" label="${job_name}_sync.2.fq" />
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57 <data format_source="input1" name="fwd_s_out" label="${job_name}_singles.1.fq">
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58 <filter>write_singles</filter>
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59 </data>
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60 <data format_source="input2" name="rev_s_out" label="${job_name}_singles.2.fq">
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61 <filter>write_singles</filter>
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62 </data>
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63 </outputs>
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64
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65 <!-- ***************************************************************** -->
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66
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67 <tests>
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69 <test>
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70 <param name="input1" value="test_R1.fq" ftype="fastq" />
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71 <param name="input2" value="test_R2.fq" ftype="fastq" />
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72 <output name="fwd_out" file="test_R1.sync.fq" compare="diff" />
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73 <output name="rev_out" file="test_R2.sync.fq" compare="diff" />
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74 </test>
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76 <test>
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77 <param name="input1" value="test_R1.fq" ftype="fastq" />
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78 <param name="input2" value="test_R2.fq" ftype="fastq" />
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79 <param name="write_singles" value="True" />
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80 <output name="fwd_out" file="test_R1.sync.fq" compare="diff" />
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81 <output name="rev_out" file="test_R2.sync.fq" compare="diff" />
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82 <output name="fwd_s_out" file="test_R1.singles.fq" compare="diff" />
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83 <output name="rev_s_out" file="test_R2.singles.fq" compare="diff" />
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84 </test>
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85
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86 </tests>
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88 <!-- ***************************************************************** -->
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90 <help>
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92 sync_reads is a utility from b2b-utils for synchronizing a pair of forward and
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93 reverse FASTQ read files. It will output a new pair of files containing only
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94 read pairs found in both input files. It can optionally output singletons from
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95 each input file as well.
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97 </help>
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99 <!-- ***************************************************************** -->
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101 <citations>
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102 </citations>
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104 </tool>
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105