Mercurial > repos > jvolkening > b2b_sync_reads

annotate sync_reads.xml @ 0:c97a821e54f3 draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
author jvolkening
date Sat, 02 Mar 2024 07:44:26 +0000
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c97a821e54f3 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
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1 <tool id="b2b_sync_reads" name="Sync paired reads" version="0.005">
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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="0.019">b2b-utils</requirement>
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9 </requirements>
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11 <!-- ***************************************************************** -->
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13 <version_command>sync_reads --version | perl -wnE'print "$1\n" for /sync_reads v(.+)/g'</version_command>
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15 <!-- ***************************************************************** -->
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17 <command detect_errors="aggressive">
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18 <![CDATA[
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20 sync_reads
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21 --fwd $input1
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22 --rev $input2
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23 --fwd_out $fwd_out
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24 --rev_out $rev_out
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25 #if str($write_singles) == 'y':
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26 --singles
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27 --fwd_singles_out $fwd_s_out
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28 --rev_singles_out $rev_s_out
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29 #end if
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31 ]]>
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32 </command>
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34 <!-- ***************************************************************** -->
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36 <inputs>
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38 <param name="job_name" type="text" size="120" value="sync_reads" label="Job narrative (added to output names)"
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39 help="Only letters, numbers and underscores (_) will be retained in this field">
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40 <sanitizer invalid_char="">
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41 <valid initial="string.letters,string.digits"><add value="_" /> </valid>
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42 </sanitizer>
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43 </param>
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44 <!-- FASTQ input(s) and options specifically for paired-end data. -->
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45 <param name="input1" format="fastqsanger,fastq" type="data" label="Forward read FASTQ file" help="Forward read FASTQ file"/>
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46 <param name="input2" format="fastqsanger,fastq" type="data" label="Reverse read FASTQ file" help="Reverse read FASTQ file"/>
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47 <param name="write_singles" type="boolean" label="Output singletons" checked="False" truevalue="y" falsevalue="n" />
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48
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49 </inputs>
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51 <!-- ***************************************************************** -->
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53 <outputs>
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54 <data format_source="input1" name="fwd_out" label="${job_name}_sync.1.fq" />
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55 <data format_source="input2" name="rev_out" label="${job_name}_sync.2.fq" />
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56 <data format_source="input1" name="fwd_s_out" label="${job_name}_singles.1.fq">
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57 <filter>write_singles</filter>
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58 </data>
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59 <data format_source="input2" name="rev_s_out" label="${job_name}_singles.2.fq">
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60 <filter>write_singles</filter>
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61 </data>
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62 </outputs>
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63
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64 <!-- ***************************************************************** -->
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66 <tests>
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68 <test expect_num_outputs="2">
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69 <param name="input1" value="test_R1.fq" ftype="fastq" />
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70 <param name="input2" value="test_R2.fq" ftype="fastq" />
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71 <output name="fwd_out" file="test_R1.sync.fq" compare="diff" />
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72 <output name="rev_out" file="test_R2.sync.fq" compare="diff" />
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73 </test>
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74
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75 <test expect_num_outputs="4">
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76 <param name="input1" value="test_R1.fq" ftype="fastq" />
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77 <param name="input2" value="test_R2.fq" ftype="fastq" />
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78 <param name="write_singles" value="True" />
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79 <output name="fwd_out" file="test_R1.sync.fq" compare="diff" />
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80 <output name="rev_out" file="test_R2.sync.fq" compare="diff" />
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81 <output name="fwd_s_out" file="test_R1.singles.fq" compare="diff" />
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82 <output name="rev_s_out" file="test_R2.singles.fq" compare="diff" />
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83 </test>
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84
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85 </tests>
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86
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87 <!-- ***************************************************************** -->
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88
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89 <help>
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90
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91 sync_reads is a utility from b2b-utils for synchronizing a pair of forward and
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92 reverse FASTQ read files. It will output a new pair of files containing only
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93 read pairs found in both input files. It can optionally output singletons from
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94 each input file as well.
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95
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96 </help>
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97
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98 <!-- ***************************************************************** -->
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99
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100 <citations>
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101 </citations>
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102
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103 </tool>
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104