Mercurial > repos > devteam > fastq_paired_end_interlacer

annotate fastq_paired_end_interlacer.xml @ 4:49b7bc41c7b0 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
author iuc
date Wed, 19 Feb 2020 16:57:03 +0000
parents a59c6f7b14c3
children 15fab8bda4e3
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49b7bc41c7b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
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1 <tool id="fastq_paired_end_interlacer" name="FASTQ interlacer" version="1.2.0.1+galaxy0">
1
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2 <description>on paired end reads</description>
3
a59c6f7b14c3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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3 <edam_topics>
a59c6f7b14c3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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4 <edam_topic>topic_0622</edam_topic>
a59c6f7b14c3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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5 </edam_topics>
a59c6f7b14c3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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6 <edam_operations>
a59c6f7b14c3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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7 <edam_operation>operation_3436</edam_operation>
a59c6f7b14c3 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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8 </edam_operations>
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49b7bc41c7b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
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9 <macros>
49b7bc41c7b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
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10 <import>macros.xml</import>
49b7bc41c7b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
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11 </macros>
49b7bc41c7b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
iuc
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12 <expand macro="requirements"/>
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13 <command><![CDATA[
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14 gx-fastq-paired-end-interlacer
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15 #if $reads.reads_selector == 'paired'
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16 '${reads.input1_file}' ${reads.input1_file.extension[len('fastq'):]} '${reads.input2_file}' ${reads.input2_file.extension[len('fastq'):]}
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17 '$outfile_pairs' '$outfile_singles'
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18 #else
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19 '${reads.reads_coll.forward}' ${reads.reads_coll.forward.extension[len('fastq'):]} '${reads.reads_coll.reverse}' ${reads.reads_coll.reverse.extension[len('fastq'):]}
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20 '$outfile_pairs_from_coll' '$outfile_singles_from_coll'
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21 #end if
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22 ]]></command>
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23 <inputs>
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24 <conditional name="reads">
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25 <param name="reads_selector" type="select" label="Type of paired-end datasets">
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26 <option value="paired">2 separate datasets</option>
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27 <option value="paired_collection">1 paired dataset collection</option>
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28 </param>
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29 <when value="paired">
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30 <param name="input1_file" type="data" format="fastqsanger,fastqcssanger,fastqsanger.gz,fastqcssanger.gz,fastqsanger.bz2,fastqcssanger.bz2" label="Left-hand mates" />
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31 <param name="input2_file" type="data" format="fastqsanger,fastqcssanger,fastqsanger.gz,fastqcssanger.gz,fastqsanger.bz2,fastqcssanger.bz2" label="Right-hand mates" />
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32 </when>
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33 <when value="paired_collection">
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34 <param name="reads_coll" type="data_collection" collection_type="paired" format="fastqsanger,fastqcssanger,fastqsanger.gz,fastqcssanger.gz,fastqsanger.bz2,fastqcssanger.bz2" label="Paired-end reads collection" />
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35 </when>
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36 </conditional>
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37 </inputs>
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38 <outputs>
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39 <!-- $input1_file.name = filename , e.g. paired_end_2_errors.fastqsanger -->
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40 <!-- $input1_file.id = ID , e.g. 10 -->
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41 <!-- $input1_file.hid = history ID, e.g. 5 -->
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42 <data name="outfile_pairs" format_source="input1_file" label="FASTQ interlacer pairs from ${on_string}">
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43 <filter>reads['reads_selector'] == 'paired'</filter>
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44 </data>
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45 <data name="outfile_singles" format_source="input1_file" label="FASTQ interlacer singles from ${on_string}">
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46 <filter>reads['reads_selector'] == 'paired'</filter>
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47 </data>
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48 <data name="outfile_pairs_from_coll" format_source="reads_coll['forward']" label="FASTQ interlacer pairs from ${on_string}">
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49 <filter>reads['reads_selector'] == 'paired_collection'</filter>
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50 </data>
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51 <data name="outfile_singles_from_coll" format_source="reads_coll['forward']" label="FASTQ interlacer singles from ${on_string}">
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52 <filter>reads['reads_selector'] == 'paired_collection'</filter>
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53 </data>
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54 </outputs>
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55 <tests>
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56 <test>
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57 <param name="reads_selector" value="paired" />
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58 <param name="input1_file" value="paired_end_1.fastqsanger" ftype="fastqsanger" />
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59 <param name="input2_file" value="paired_end_2.fastqsanger" ftype="fastqsanger" />
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60 <output name="outfile_pairs" file="paired_end_merged.fastqsanger" ftype="fastqsanger" />
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61 <output name="outfile_singles" file="paired_end_merged_singles.fastqsanger" ftype="fastqsanger" />
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62 </test>
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63 <test>
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64 <param name="reads_selector" value="paired" />
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65 <param name="input1_file" value="paired_end_1_errors.fastqsanger" ftype="fastqsanger" />
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66 <param name="input2_file" value="paired_end_2_errors.fastqsanger" ftype="fastqsanger" />
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67 <output name="outfile_pairs" file="paired_end_merged_cleaned.fastqsanger" ftype="fastqsanger" />
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68 <output name="outfile_singles" file="paired_end_merged_cleaned_singles.fastqsanger" ftype="fastqsanger" />
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69 </test>
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70 <test>
2
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71 <param name="reads_selector" value="paired" />
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72 <param name="input1_file" value="paired_end_1_errors.fastqsanger.gz" ftype="fastqsanger.gz" />
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73 <param name="input2_file" value="paired_end_2_errors.fastqsanger.gz" ftype="fastqsanger.gz" />
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74 <output name="outfile_pairs" file="paired_end_merged_cleaned.fastqsanger" ftype="fastqsanger.gz" decompress="true" />
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75 <output name="outfile_singles" file="paired_end_merged_cleaned_singles.fastqsanger" ftype="fastqsanger.gz" decompress="true" />
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76 </test>
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77 <test>
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78 <param name="reads_selector" value="paired" />
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79 <param name="input1_file" value="paired_end_1_errors.fastqsanger.bz2" ftype="fastqsanger.bz2" />
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80 <param name="input2_file" value="paired_end_2_errors.fastqsanger.bz2" ftype="fastqsanger.bz2" />
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81 <output name="outfile_pairs" file="paired_end_merged_cleaned.fastqsanger" ftype="fastqsanger.bz2" decompress="true" />
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82 <output name="outfile_singles" file="paired_end_merged_cleaned_singles.fastqsanger" ftype="fastqsanger.bz2" decompress="true" />
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83 </test>
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84 <test>
1
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85 <param name="reads_selector" value="paired_collection" />
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86 <param name="reads_coll">
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87 <collection type="paired">
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88 <element name="forward" value="paired_end_1.fastqsanger" ftype="fastqsanger" />
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89 <element name="reverse" value="paired_end_2.fastqsanger" ftype="fastqsanger" />
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90 </collection>
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91 </param>
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92 <output name="outfile_pairs_from_coll" file="paired_end_merged.fastqsanger" ftype="fastqsanger" />
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93 <output name="outfile_singles_from_coll" file="paired_end_merged_singles.fastqsanger" ftype="fastqsanger" />
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94 </test>
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95 </tests>
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96 <help><![CDATA[
0
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97 **What it does**
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98
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99 This tool joins paired end FASTQ reads from two separate files, one with the left mates and one with the right mates, into a single files where left mates alternate with their right mates. The join is performed using sequence identifiers, allowing the two files to contain differing ordering. If a sequence identifier does not appear in both files, it is included in a separate file.
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100
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101 Sequence identifiers with /1 and /2 appended override the left-hand and right-hand designation; i.e. if the reads end with /1 and /2, the read containing /1 will be used as the left-hand read and the read containing /2 will be used as the right-hand read. Sequences without this designation will follow the left-hand and right-hand settings set by the user.
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102
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103 -----
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104
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105 **Input**
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106
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107 Left-hand mates, for example::
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108
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109 @1539:931/1
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110 ACTTCCCGCGCGTGAAGGCGCCGGCAAACGAGGCTCGGGAAGGGGCTCCCG
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111 +1539:931/1
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112 BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
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113
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114 Right-hand mates, for example::
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115
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116 @1539:931/2
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117 CGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT
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118 +1539:931/2
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119 WNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
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120
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121 -----
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122
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123 **Output**
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124
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125 A multiple-fastq file containing interlaced left and right paired reads::
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126
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127 @1539:931/1
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128 ACTTCCCGCGCGTGAAGGCGCCGGCAAACGAGGCTCGGGAAGGGGCTCCCG
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129 +1539:931/1
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130 BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
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131 @1539:931/2
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132 CGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT
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133 +1539:931/2
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134 WNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
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135
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136 A multiple-fastq file containing reads that have no mate is also produced.
1
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137 ]]></help>
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138 <citations>
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139 <citation type="doi">10.1093/bioinformatics/btq281</citation>
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140 </citations>
0
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141 </tool>