Mercurial > repos > jvolkening > b2b_fq_deinterleave

annotate fq_deinterleave.xml @ 1:3cab918bc851 draft default tip

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit f66b297dfee0d16df8f185c075fe349b8c6b3203
author jvolkening
date Fri, 08 Mar 2024 01:49:12 +0000
parents b42eb9ff6a8c
children
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rev   line source
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3cab918bc851 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit f66b297dfee0d16df8f185c075fe349b8c6b3203
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1 <tool id="b2b_@TOOL_NAME@" name="De-interleave reads"
0
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2 version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="MIT" profile="21.01">
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3 <description>De-interleave paired FASTQ files</description>
0
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4 <macros>
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5 <token name="@TOOL_NAME@">fq_deinterleave</token>
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6 <token name="@TOOL_VERSION@">0.202</token>
1
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7 <token name="@VERSION_SUFFIX@">2</token>
0
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8 <import>macros.xml</import>
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9 </macros>
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10 <edam_topics>
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11 <edam_topic>topic_0080</edam_topic> <!-- Sequence analysis -->
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12 </edam_topics>
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13 <edam_operations>
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14 <edam_operation>operation_0335</edam_operation> <!-- Formatting -->
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15 </edam_operations>
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16 <expand macro="requirements" />
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17 <expand macro="version_command" />
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18
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19 <!-- ***************************************************************** -->
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21 <command detect_errors="aggressive">
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22 <![CDATA[
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23
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24 fq_deinterleave
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25 --in $input
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26 --1 $output1
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27 --2 $output2
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28 $check
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29 $norename
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30 $compress_output
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31 ## (see e.g. samtools wrappers, which also need to force overwrite)
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32 --force
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33
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34 ]]>
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35 </command>
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36
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37 <!-- ***************************************************************** -->
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38
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39 <inputs>
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40 <param name="input"
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41 type="data"
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42 format="fastqsanger,fastq,fastqsanger.gz,fastq.gz"
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43 label="Interleaved reads"
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44 help="FASTQ file" />
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45 <param argument="--check"
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46 type="boolean"
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47 label="Check names"
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48 checked="true"
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49 truevalue="--check"
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50 falsevalue=""
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51 help="Verify that paired names match" />
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52 <param argument="--norename"
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53 type="boolean"
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54 label="Don't rename"
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55 checked="False"
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56 truevalue="--norename"
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57 falsevalue=""
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58 help="Don't strip /1 and /2 suffixes from end of read names" />
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59 <param name="compress_output"
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60 type="boolean"
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61 checked="true"
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62 truevalue="--compress"
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63 falsevalue=""
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64 label="Compress output" />
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65 </inputs>
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66
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67 <!-- ***************************************************************** -->
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68
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69 <outputs>
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70 <data name="output1" format="fastq.gz" label="${tool.name} on ${on_string} (fwd)">
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71 <change_format>
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72 <when input="compress_output" value="" format="fastq" />
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73 </change_format>
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74 </data>
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75 <data name="output2" format="fastq.gz" label="${tool.name} on ${on_string} (rev)">
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76 <change_format>
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77 <when input="compress_output" value="" format="fastq" />
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78 </change_format>
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79 </data>
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80 </outputs>
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81
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82 <!-- ***************************************************************** -->
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83
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84 <tests>
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85
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86 <!-- default options -->
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87 <test>
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88 <param name="input" value="test.il.fq" />
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89 <output name="output1" file="test_R1.rename.fq" compare="diff" ftype="fastq.gz" decompress="true" />
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90 <output name="output2" file="test_R2.rename.fq" compare="diff" ftype="fastq.gz" decompress="true" />
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91 <assert_command>
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92 <not_has_text text="--norename " />
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93 </assert_command>
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94 </test>
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95 <!-- mismatched inputs -->
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96 <test expect_failure="true">
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97 <param name="input" value="test.il.bad.fq" />
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98 <param name="check" value="true" />
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99 </test>
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100 <!-- other options -->
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101 <test expect_num_outputs="2">
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102 <param name="input" value="test.il.fq" />
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103 <param name="check" value="true" />
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104 <param name="norename" value="true" />
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105 <param name="compress_output" value="false" />
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106 <output name="output1" file="test_R1.sync.fq" compare="diff" ftype="fastq" />
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107 <output name="output2" file="test_R2.sync.fq" compare="diff" ftype="fastq" />
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108 <assert_command>
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109 <has_text text="--check" />
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110 <has_text text="--norename" />
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111 </assert_command>
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112 </test>
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113
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114 </tests>
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115
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116 <!-- ***************************************************************** -->
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117
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118 <help>
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119
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120 sync_reads is a utility from b2b-utils for synchronizing a pair of forward and
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121 reverse FASTQ read files. It will output a new pair of files containing only
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122 read pairs found in both input files. It can optionally output singletons from
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123 each input file as well.
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124
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125 </help>
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126
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127 <!-- ***************************************************************** -->
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128
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129 <citations>
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130 </citations>
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131
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132 </tool>
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133