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annotate fastq_paired_end_interlacer.xml @ 2:1adeef975783 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit 28c441e8aa66a55d276b0f6325d34086eb715872
author devteam
date Sat, 07 Oct 2017 10:00:35 -0400
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children a59c6f7b14c3
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1adeef975783 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit 28c441e8aa66a55d276b0f6325d34086eb715872
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1 <tool id="fastq_paired_end_interlacer" name="FASTQ interlacer" version="1.2.0.1">
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2 <description>on paired end reads</description>
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3 <requirements>
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4 <requirement type="package" version="1.1.2">galaxy_sequence_utils</requirement>
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5 </requirements>
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6 <command><![CDATA[
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7 gx-fastq-paired-end-interlacer
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8 #if $reads.reads_selector == 'paired'
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9 '${reads.input1_file}' ${reads.input1_file.extension[len('fastq'):]} '${reads.input2_file}' ${reads.input2_file.extension[len('fastq'):]}
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10 '$outfile_pairs' '$outfile_singles'
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11 #else
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12 '${reads.reads_coll.forward}' ${reads.reads_coll.forward.extension[len('fastq'):]} '${reads.reads_coll.reverse}' ${reads.reads_coll.reverse.extension[len('fastq'):]}
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13 '$outfile_pairs_from_coll' '$outfile_singles_from_coll'
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14 #end if
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15 ]]></command>
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16 <inputs>
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17 <conditional name="reads">
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18 <param name="reads_selector" type="select" label="Type of paired-end datasets">
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19 <option value="paired">2 separate datasets</option>
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20 <option value="paired_collection">1 paired dataset collection</option>
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21 </param>
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22 <when value="paired">
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23 <param name="input1_file" type="data" format="fastqsanger,fastqcssanger,fastqsanger.gz,fastqcssanger.gz,fastqsanger.bz2,fastqcssanger.bz2" label="Left-hand mates" />
e0a8fba7ed2f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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24 <param name="input2_file" type="data" format="fastqsanger,fastqcssanger,fastqsanger.gz,fastqcssanger.gz,fastqsanger.bz2,fastqcssanger.bz2" label="Right-hand mates" />
e0a8fba7ed2f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit f2582539542b33240234e8ea6093e25d0aee9b6a
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25 </when>
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26 <when value="paired_collection">
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27 <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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28 </when>
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29 </conditional>
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30 </inputs>
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31 <outputs>
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32 <!-- $input1_file.name = filename , e.g. paired_end_2_errors.fastqsanger -->
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33 <!-- $input1_file.id = ID , e.g. 10 -->
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34 <!-- $input1_file.hid = history ID, e.g. 5 -->
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35 <data name="outfile_pairs" format_source="input1_file" label="FASTQ interlacer pairs from ${on_string}">
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36 <filter>reads['reads_selector'] == 'paired'</filter>
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37 </data>
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38 <data name="outfile_singles" format_source="input1_file" label="FASTQ interlacer singles from ${on_string}">
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39 <filter>reads['reads_selector'] == 'paired'</filter>
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40 </data>
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41 <data name="outfile_pairs_from_coll" format_source="reads_coll['forward']" label="FASTQ interlacer pairs from ${on_string}">
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42 <filter>reads['reads_selector'] == 'paired_collection'</filter>
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43 </data>
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44 <data name="outfile_singles_from_coll" format_source="reads_coll['forward']" label="FASTQ interlacer singles from ${on_string}">
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45 <filter>reads['reads_selector'] == 'paired_collection'</filter>
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46 </data>
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47 </outputs>
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48 <tests>
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49 <test>
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50 <param name="reads_selector" value="paired" />
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51 <param name="input1_file" value="paired_end_1.fastqsanger" ftype="fastqsanger" />
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52 <param name="input2_file" value="paired_end_2.fastqsanger" ftype="fastqsanger" />
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53 <output name="outfile_pairs" file="paired_end_merged.fastqsanger" ftype="fastqsanger" />
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54 <output name="outfile_singles" file="paired_end_merged_singles.fastqsanger" ftype="fastqsanger" />
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55 </test>
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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_errors.fastqsanger" ftype="fastqsanger" />
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59 <param name="input2_file" value="paired_end_2_errors.fastqsanger" ftype="fastqsanger" />
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60 <output name="outfile_pairs" file="paired_end_merged_cleaned.fastqsanger" ftype="fastqsanger" />
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61 <output name="outfile_singles" file="paired_end_merged_cleaned_singles.fastqsanger" ftype="fastqsanger" />
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62 </test>
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63 <test>
2
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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.gz" ftype="fastqsanger.gz" />
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66 <param name="input2_file" value="paired_end_2_errors.fastqsanger.gz" ftype="fastqsanger.gz" />
1adeef975783 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer commit 28c441e8aa66a55d276b0f6325d34086eb715872
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67 <output name="outfile_pairs" file="paired_end_merged_cleaned.fastqsanger" ftype="fastqsanger.gz" decompress="true" />
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68 <output name="outfile_singles" file="paired_end_merged_cleaned_singles.fastqsanger" ftype="fastqsanger.gz" decompress="true" />
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69 </test>
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70 <test>
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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.bz2" ftype="fastqsanger.bz2" />
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73 <param name="input2_file" value="paired_end_2_errors.fastqsanger.bz2" ftype="fastqsanger.bz2" />
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74 <output name="outfile_pairs" file="paired_end_merged_cleaned.fastqsanger" ftype="fastqsanger.bz2" decompress="true" />
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75 <output name="outfile_singles" file="paired_end_merged_cleaned_singles.fastqsanger" ftype="fastqsanger.bz2" decompress="true" />
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76 </test>
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77 <test>
1
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78 <param name="reads_selector" value="paired_collection" />
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79 <param name="reads_coll">
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80 <collection type="paired">
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81 <element name="forward" value="paired_end_1.fastqsanger" ftype="fastqsanger" />
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82 <element name="reverse" value="paired_end_2.fastqsanger" ftype="fastqsanger" />
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83 </collection>
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84 </param>
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85 <output name="outfile_pairs_from_coll" file="paired_end_merged.fastqsanger" ftype="fastqsanger" />
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86 <output name="outfile_singles_from_coll" file="paired_end_merged_singles.fastqsanger" ftype="fastqsanger" />
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87 </test>
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88 </tests>
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89 <help><![CDATA[
0
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90 **What it does**
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91
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92 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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93
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94 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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95
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96 -----
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97
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98 **Input**
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99
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100 Left-hand mates, for example::
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101
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102 @1539:931/1
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103 ACTTCCCGCGCGTGAAGGCGCCGGCAAACGAGGCTCGGGAAGGGGCTCCCG
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104 +1539:931/1
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105 BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
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106
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107 Right-hand mates, for example::
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108
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109 @1539:931/2
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110 CGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT
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111 +1539:931/2
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112 WNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
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113
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114 -----
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115
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116 **Output**
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117
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118 A multiple-fastq file containing interlaced left and right paired reads::
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119
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120 @1539:931/1
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121 ACTTCCCGCGCGTGAAGGCGCCGGCAAACGAGGCTCGGGAAGGGGCTCCCG
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122 +1539:931/1
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123 BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
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124 @1539:931/2
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125 CGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT
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126 +1539:931/2
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127 WNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
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128
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129 A multiple-fastq file containing reads that have no mate is also produced.
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130 ]]></help>
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131 <citations>
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132 <citation type="doi">10.1093/bioinformatics/btq281</citation>
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133 </citations>
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134 </tool>