Mercurial > repos > jvolkening > b2b_sync_reads

annotate sync_reads.xml @ 1:e8df16b34fec draft default tip

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
author jvolkening
date Fri, 08 Mar 2024 00:44:37 +0000
parents c97a821e54f3
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 <tool id="b2b_sync_reads" name="Sync paired reads"
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2 version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="MIT" profile="21.01">
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4 <description>Synchronize trimmed/filtered read-pair set</description>
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5 <macros>
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6 <token name="@TOOL_NAME@">sync_reads</token>
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7 <token name="@TOOL_VERSION@">0.005</token>
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8 <token name="@VERSION_SUFFIX@">1</token>
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9 <import>macros.xml</import>
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10 </macros>
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11 <edam_topics>
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12 <edam_topic>topic_0080</edam_topic> <!-- Sequence analysis -->
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13 </edam_topics>
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14 <edam_operations>
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15 <edam_operation>operation_0335</edam_operation> <!-- Formatting -->
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16 </edam_operations>
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17 <expand macro="requirements" />
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18 <expand macro="version_command" />
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20 <!-- ***************************************************************** -->
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22 <command detect_errors="aggressive">
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23 <![CDATA[
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25 sync_reads
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26 --fwd $input1
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27 --rev $input2
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28 --fwd_out $fwd_out
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29 --rev_out $rev_out
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30 #if str($write_singles) == 'y':
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31 --singles
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32 --fwd_singles_out $fwd_s_out
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33 --rev_singles_out $rev_s_out
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34 #end if
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35
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36 ]]>
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37 </command>
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39 <!-- ***************************************************************** -->
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41 <inputs>
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43 <param name="job_name" type="text" size="120" value="sync_reads" label="Job narrative (added to output names)"
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44 help="Only letters, numbers and underscores (_) will be retained in this field">
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45 <sanitizer invalid_char="">
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46 <valid initial="string.letters,string.digits"><add value="_" /> </valid>
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47 </sanitizer>
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48 </param>
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49 <!-- FASTQ input(s) and options specifically for paired-end data. -->
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50 <param name="input1" format="fastqsanger,fastq" type="data" label="Forward read FASTQ file" help="Forward read FASTQ file"/>
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51 <param name="input2" format="fastqsanger,fastq" type="data" label="Reverse read FASTQ file" help="Reverse read FASTQ file"/>
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52 <param name="write_singles" type="boolean" label="Output singletons" checked="False" truevalue="y" falsevalue="n" />
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53
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54 </inputs>
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55
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56 <!-- ***************************************************************** -->
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57
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58 <outputs>
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59 <data format_source="input1" name="fwd_out" label="${job_name}_sync.1.fq" />
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60 <data format_source="input2" name="rev_out" label="${job_name}_sync.2.fq" />
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61 <data format_source="input1" name="fwd_s_out" label="${job_name}_singles.1.fq">
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62 <filter>write_singles</filter>
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63 </data>
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64 <data format_source="input2" name="rev_s_out" label="${job_name}_singles.2.fq">
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65 <filter>write_singles</filter>
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66 </data>
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67 </outputs>
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68
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69 <!-- ***************************************************************** -->
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71 <tests>
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72
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73 <test expect_num_outputs="2">
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74 <param name="input1" value="test_R1.fq" ftype="fastq" />
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75 <param name="input2" value="test_R2.fq" ftype="fastq" />
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76 <output name="fwd_out" file="test_R1.sync.fq" compare="diff" />
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77 <output name="rev_out" file="test_R2.sync.fq" compare="diff" />
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78 </test>
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79
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80 <test expect_num_outputs="4">
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81 <param name="input1" value="test_R1.fq" ftype="fastq" />
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82 <param name="input2" value="test_R2.fq" ftype="fastq" />
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83 <param name="write_singles" value="True" />
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84 <output name="fwd_out" file="test_R1.sync.fq" compare="diff" />
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85 <output name="rev_out" file="test_R2.sync.fq" compare="diff" />
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86 <output name="fwd_s_out" file="test_R1.singles.fq" compare="diff" />
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87 <output name="rev_s_out" file="test_R2.singles.fq" compare="diff" />
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88 </test>
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89
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90 </tests>
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91
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92 <!-- ***************************************************************** -->
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93
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94 <help>
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95
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96 sync_reads is a utility from b2b-utils for synchronizing a pair of forward and
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97 reverse FASTQ read files. It will output a new pair of files containing only
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98 read pairs found in both input files. It can optionally output singletons from
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99 each input file as well.
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100
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101 </help>
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102
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103 <!-- ***************************************************************** -->
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104
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105 <citations>
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106 </citations>
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107
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108 </tool>
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109