Mercurial > repos > jvolkening > b2b_fq_interleave

annotate fq_interleave.xml @ 0:6530b8a73225 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 00:48:17 +0000
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0
6530b8a73225 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9260aa02a5f703bce63d2db5b69003df9be371ac
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1 <tool id="b2b_@TOOL_NAME@" name="Interleave reads"
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2 version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="MIT" profile="20.01">
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3 <description>Interleaved paired FASTQ files</description>
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4 <macros>
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5 <token name="@TOOL_NAME@">fq_interleave</token>
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6 <token name="@TOOL_VERSION@">0.202</token>
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7 <token name="@VERSION_SUFFIX@">1</token>
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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="requirement_pigz" />
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18 </expand>
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19 <expand macro="version_command" />
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20
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21 <!-- ***************************************************************** -->
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23 <command detect_errors="aggressive" strict="true">
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24 <![CDATA[
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25
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26 set -o pipefail;
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27
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28 fq_interleave
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29 --1 $input1
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30 --2 $input2
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31 $check
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32 $rename
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33 $compress_output
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34 > $output
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35
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36 ]]>
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37 </command>
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38
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39 <!-- ***************************************************************** -->
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40
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41 <inputs>
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42 <param name="input1"
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43 type="data"
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44 format="fastqsanger,fastq,fastqsanger.gz,fastq.gz"
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45 label="Forward reads"
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46 help="Forward read FASTQ file" />
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47 <param name="input2"
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48 type="data"
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49 format="fastqsanger,fastq,fastqsanger.gz,fastq.gz"
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50 label="Reverse reads"
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51 help="Reverse read FASTQ file" />
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52 <param argument="--check"
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53 type="boolean"
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54 label="Check names"
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55 checked="False"
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56 truevalue="--check"
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57 falsevalue=""
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58 help="Verify that paired names match" />
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59 <param argument="--rename"
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60 type="boolean"
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61 label="Rename"
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62 checked="False"
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63 truevalue="--rename"
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64 falsevalue=""
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65 help="Ensure /1 and /2 at end of read names" />
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66 <param name="compress_output"
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67 type="boolean"
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68 checked="true"
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69 truevalue="@PIPE_PIGZ@"
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70 falsevalue=""
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71 label="Compress output" />
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72 </inputs>
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73
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74 <!-- ***************************************************************** -->
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75
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76 <outputs>
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77 <data name="output" format="fastq.gz">
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78 <change_format>
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79 <when input="compress_output" value="" format="fastq" />
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80 </change_format>
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81 </data>
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82 </outputs>
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83
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84 <!-- ***************************************************************** -->
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85
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86 <tests>
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87
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88 <!-- default options -->
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89 <test expect_num_outputs="1">
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90 <param name="input1" value="test_R1.sync.fq" ftype="fastq" />
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91 <param name="input2" value="test_R2.sync.fq" ftype="fastq" />
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92 <output name="output" file="test.il.fq" compare="diff" ftype="fastq.gz" decompress="true"/>
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93 <assert_command>
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94 <not_has_text text="--check " />
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95 <not_has_text text="--rename " />
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96 </assert_command>
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97 </test>
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98 <!-- mismatched inputs -->
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99 <test expect_failure="true">
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100 <param name="input1" value="test_R1.fq" ftype="fastq" />
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101 <param name="input2" value="test_R2.fq" ftype="fastq" />
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102 <param name="check" value="true" />
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103 </test>
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104 <!-- other options -->
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105 <test expect_num_outputs="1">
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106 <param name="input1" value="test_R1.sync.fq" ftype="fastq" />
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107 <param name="input2" value="test_R2.sync.fq" ftype="fastq" />
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108 <param name="check" value="true" />
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109 <param name="rename" value="true" />
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110 <param name="compress_output" value="false" />
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111 <output name="output" file="test.il.fq" compare="diff" ftype="fastq" />
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112 <assert_command>
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113 <has_text text="--check" />
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114 <has_text text="--rename" />
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115 </assert_command>
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116 </test>
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117
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118 </tests>
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119
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120 <!-- ***************************************************************** -->
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121
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122 <help>
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123
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124 sync_reads is a utility from b2b-utils for synchronizing a pair of forward and
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125 reverse FASTQ read files. It will output a new pair of files containing only
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126 read pairs found in both input files. It can optionally output singletons from
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127 each input file as well.
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128
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129 </help>
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130
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131 <!-- ***************************************************************** -->
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132
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133 <citations>
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134 </citations>
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135
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136 </tool>
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137