Mercurial > repos > iuc > stacks2_shortreads

annotate stacks_shortreads.xml @ 0:ad7a60726fc3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
author iuc
date Mon, 01 Jul 2019 11:02:39 -0400
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ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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1 <!-- this is essentially a copy of stacks_procrad minus the unsupported options -->
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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2 <tool id="stacks2_shortreads" name="Stacks2: process shortreads" profile="@PROFILE@" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@">
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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3 <description>fast cleaning of randomly sheared genomic or transcriptomic data</description>
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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4 <macros>
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5 <import>macros.xml</import>
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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6 <import>macros_process.xml</import>
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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7 </macros>
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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8 <expand macro="requirements"/>
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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9 <expand macro="version_cmd"/>
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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10 <command detect_errors="aggressive"><![CDATA[
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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11 @FASTQ_INPUT_FUNCTIONS@
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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12
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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13 mkdir stacks_inputs stacks_outputs &&
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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15 #set ($link_command, $inputype) = $fastq_input_nonbatch( $input_type.fqinputs, $input_type.input_type_select, "_R%d_0" )
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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16 $link_command
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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19 process_shortreads
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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21 @PROCESS_IOOPTIONS@
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22 @PROCESS_FILTER@
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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23 @COMMON_ADVANCED@
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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24 @RESCUE_BARCODE@
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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25 @PROCESS_ADAPTER@
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26
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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27 ## advanced options not shared between shortreads and radtags
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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28 $options_advanced.no_read_trimming
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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29 $options_advanced.mate_pair
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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30 $options_advanced.no_overhang
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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31
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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32 #if $output_log
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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33 && mv stacks_outputs/process_shortreads.log $output_log
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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34 #end if
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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35 @PROCESS_FASTQ_POSTPROC@
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36 ]]></command>
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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37
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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38 <inputs>
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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39 <expand macro="fastq_input_bc_file" multiple="true" listtype="list:paired"/>
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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40 <section name="options_advanced" title="advanced options" expanded="False">
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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41 <expand macro="common_advanced"/>
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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42 <param argument="--no_read_trimming" type="boolean" checked="false" truevalue="--no_read_trimming" falsevalue="" label="Do not trim low quality reads, just discard them" />
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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43 <param argument="--mate-pair" name="mate_pair" type="boolean" checked="false" truevalue="--mate-pair" falsevalue="" label="Raw reads are circularized mate-pair data, first read will be reverse complemented" />
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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44 <param argument="--no_overhang" type="boolean" checked="false" truevalue="--no_overhang" falsevalue="" label="Data does not contain an overhang nucleotide between barcode and seqeunce" />
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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45 <expand macro="rescue_barcode"/>
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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46 <expand macro="process_adapter"/>
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47 </section>
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48 <expand macro="process_filter"/>
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49 <expand macro="process_output_types"/>
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50 </inputs>
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51
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52 <outputs>
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53 <data format="txt" name="output_log" label="${tool.name} on ${on_string} log file" from_work_dir="stacks_outputs/process_shortreads.log" />
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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54 <expand macro="process_outputs"/>
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55 </outputs>
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56
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57 <tests>
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58 <!-- test single end, default options -->
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59 <test>
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60 <param name="input_type|input_type_select" value="single"/>
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61 <param name="input_type|fqinputs" ftype="fastqsanger" value="procrad/R1.fq"/>
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62 <param name="input_type|barcode_encoding" value="--inline_null"/>
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63 <param name="barcode" value="procrad/barcodes"/>
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64 <param name="add_log" value="yes" />
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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65 <output name="output_log" file="shortreads/process_shortreads.out" lines_diff="4"/>
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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66 <output_collection name="demultiplexed" count="40">
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67 <element name="PopA_01" file="shortreads/PopA_01.fq" ftype="fastqsanger" />
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68 </output_collection>
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69 </test>
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70 <!-- test single end, default options -->
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71 <test>
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72 <param name="input_type|input_type_select" value="paired"/>
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73 <param name="input_type|fqinputs">
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74 <collection type="list:paired">
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75 <element name="reads">
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76 <collection type="paired">
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77 <element name="forward" value="procrad/R1.fq" ftype="fastqsanger" />
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78 <element name="reverse" value="procrad/R2.fq" ftype="fastqsanger"/>
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79 </collection>
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80 </element>
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81 </collection>
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82 </param>
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83 <param name="input_type|barcode_encoding" value="--inline_null"/>
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84 <param name="barcode" value="procrad/barcodes"/>
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85 <param name="capture" value="true"/>
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86 <param name="no_read_trimming" value="--no_read_trimming" />
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87 <param name="mate_pair" value="--mate-pair" />
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88 <param name="no_overhang" value="--no_overhang" />
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89 <param name="outype" value="gzfastq"/>
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90 <param name="add_log" value="yes" />
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91 <assert_command>
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92 <has_text text="--no_read_trimming" />
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93 <has_text text="--mate-pair" />
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94 <has_text text="--no_overhang" />
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95 </assert_command>
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96 <output name="output_log" file="shortreads/process_shortreads.out" compare="sim_size"/>
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97 <output_collection name="demultiplexed_paired" type="list:paired" count="40">
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98 <element name="PopA_01">
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99 <element name="forward" value="shortreads/PopA_01.forward.fq.gz" ftype="fastqsanger.gz" compare="sim_size"/>
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100 <element name="reverse" value="shortreads/PopA_01.reverse.fq.gz" ftype="fastqsanger.gz" compare="sim_size"/>
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101 </element>
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102 </output_collection>
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103 <output_collection name="remaining" type="list:paired" count="40">
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104 <element name="PopA_01">
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105 <element name="forward" file="shortreads/PopA_01.rem.forward.fq.gz" ftype="fastqsanger.gz"/>
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106 <element name="reverse" file="shortreads/PopA_01.rem.reverse.fq.gz" ftype="fastqsanger.gz"/>
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107 </element>
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108 </output_collection>
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109 <output_collection name="discarded_paired" type="list:paired" count="1">
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110 <element name="reads">
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111 <element name="forward" file="shortreads/reads.forward.fq" ftype="fastqsanger"/>
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112 <element name="reverse" file="shortreads/reads.forward.fq" ftype="fastqsanger"/>
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113 </element>
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114 </output_collection>
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115 </test>
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116 </tests>
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117 <help>
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118 <![CDATA[
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119 .. class:: infomark
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120
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121 **What it does**
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122
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123 Performs the same task as process_radtags for fast cleaning of randomly sheared genomic or transcriptomic data, not for RAD data.
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124
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125 **Help**
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126
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127 Input files:
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128
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129 - FASTQ
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130
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131 - Barcode File Format
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132
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133 The barcode file is a very simple format:
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134
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135 ======= ===========
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136 Barcode Sample name
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137 ======= ===========
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138 ATGGGG PopA_01
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139 GGGTAA PopA_02
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140 AGGAAA PopA_03
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141 TTTAAG PopA_04
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142 GGTGTG PopA_05
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143 TGATGT PopA_06
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144 ======= ===========
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145
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146 Combinatorial barcodes are specified, one per column, separated by a tab:
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147
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148 ======== ======== ===========
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149 Barcode1 Barcode2 Sample name
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150 ======== ======== ===========
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151 CGATA ACGTA PopA_01
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152 CGGCG CGTA PopA_02
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153 GAAGC CGTA PopA_03
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154 GAGAT CGTA PopA_04
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155 CGATA AGCA PopA_05
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156 CGGCG AGCA PopA_06
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157 ======== ======== ===========
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158
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159 @STACKS_INFOS@
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160 ]]>
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161 </help>
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162 <expand macro="citation" />
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163 </tool>