Mercurial > repos > matthias > stacks2_tsv2bam

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 82e7263f3e57a29362d981e36b82b82063f12ac3
author matthias
date Tue, 25 Jun 2019 10:58:48 -0400
parents 852044374da1
children
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1 <tool id="stacks2_tsv2bam" name="Stacks2: tsv2bam" profile="@PROFILE@" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@">
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2 <description>Sort reads by RAD locus</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="version_cmd"/>
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8 <command detect_errors="aggressive"><![CDATA[
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9 @FASTQ_INPUT_FUNCTIONS@
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11 mkdir stacks_inputs stacks_outputs &&
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12
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13 @LINK_STACKS_INPUT@
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14 @LINK_CAT_INPUT@
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15 @LINK_MATCHES_INPUT@
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17 ## link fastq files into stacks_inputs/
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18 #set $paired_reads=False
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19 #for $sample in $input_type.fqinputs:
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20 #if not $sample:
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21 #continue
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22 #end if
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23 #set $paired_reads=True
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24 #set ($link_cmd, $data_path, $name, $inputype) = $fastq_input_foo($sample, "reverse", ".2")
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25 $link_cmd
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26 #end for
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27
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28 tsv2bam
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29 -P stacks_inputs
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30 #if $popmap
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31 -M '$popmap'
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32 #else
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33 #for $sample in $samples
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34 -s '$sample'
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35 #end for
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36 #end if
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37 #if $paired_reads
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38 --pe-reads-dir stacks_inputs
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39 #end if
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40 -t \${GALAXY_SLOTS:-1}
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41 ## tsv2bam writes to stdout and creates a log file
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42 ## - make stdout stderr
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43 ## - move the additional log file
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44 2>&1
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45
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46 #if $output_log
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47 && mv stacks_inputs/tsv2bam.log $output_log
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48 #end if
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49 && mv stacks_inputs/*matches.bam stacks_outputs
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50 ]]></command>
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51
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52 <inputs>
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53 <expand macro="input_stacks_macro"/>
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54 <expand macro="input_cat_macro"/>
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55 <expand macro="input_matches_macro"/>
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56 <!-- TODO add BAM? -->
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57 <expand macro="fastq_input" fastq_optional="true" se_option="reverse reads" help="Paired end data or reverse reads. If a paired list is provided only the reverse reads are used in tsv2bam. Leave selection empty if you analyse single end data."/>
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58 <param name="popmap" type="data" format="tabular,txt" label="Population map" help="If set, matching will be done only for samples listed in this file" optional="true" argument="-M" />
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59 <expand macro="in_log"/>
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60 </inputs>
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61
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62 <outputs>
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63 <expand macro="out_log"/>
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64 <expand macro="tsv2bam_outputs_macro"/>
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65 </outputs>
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66
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67 <tests>
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68 <!-- test wo paired end data -->
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69 <test>
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70 <param name="input_cat">
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71 <collection type="list">
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72 <element name="catalog.alleles" ftype="tabular" value="cstacks/catalog.alleles.tsv" />
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73 <element name="catalog.snps" ftype="tabular" value="cstacks/catalog.snps.tsv" />
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74 <element name="catalog.tags" ftype="tabular" value="cstacks/catalog.tags.tsv" />
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75 </collection>
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76 </param>
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77 <param name="input_stacks">
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78 <collection type="list">
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79 <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv" />
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80 <element name="PopA_01.snps" ftype="tabular" value="ustacks/PopA_01.snps.tsv" />
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81 <element name="PopA_01.tags" ftype="tabular" value="ustacks/PopA_01.tags.tsv" />
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82 <element name="PopA_02.alleles" ftype="tabular" value="ustacks/PopA_02.alleles.tsv" />
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83 <element name="PopA_02.snps" ftype="tabular" value="ustacks/PopA_02.snps.tsv" />
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84 <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv" />
0
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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85 </collection>
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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86 </param>
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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87 <param name="input_matches">
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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88 <collection type="list">
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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89 <element name="PopA_01.matches" ftype="tabular" value="sstacks/PopA_01.matches.tsv" />
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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90 <element name="PopA_02.matches" ftype="tabular" value="sstacks/PopA_02.matches.tsv" />
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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91 </collection>
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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92 </param>
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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93 <param name="add_log" value="yes" />
5
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94 <output name="output_log" ftype="txt" file="tsv2bam/tsv2bam.log" lines_diff="14"/>
0
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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95 <output_collection name="bams" type="list" count="2">
4
60c1c4d7d2c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
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96 <element name="PopA_01.matches" file="tsv2bam/PopA_01.matches.bam" ftype="bam"/>
60c1c4d7d2c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
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97 <element name="PopA_02.matches" file="tsv2bam/PopA_02.matches.bam" ftype="bam"/>
0
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98 </output_collection>
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99 </test>
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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100 <!-- test w popmap, w reverse reads as multiple selection -->
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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101 <test>
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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102 <param name="input_cat">
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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103 <collection type="list">
4
60c1c4d7d2c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
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104 <element name="catalog.alleles" ftype="tabular" value="cstacks/catalog.alleles.tsv" />
60c1c4d7d2c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
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105 <element name="catalog.snps" ftype="tabular" value="cstacks/catalog.snps.tsv" />
60c1c4d7d2c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
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106 <element name="catalog.tags" ftype="tabular" value="cstacks/catalog.tags.tsv" />
0
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107 </collection>
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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108 </param>
4
60c1c4d7d2c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
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109 <param name="input_stacks">
0
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110 <collection type="list">
4
60c1c4d7d2c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
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111 <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv" />
60c1c4d7d2c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
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112 <element name="PopA_01.snps" ftype="tabular" value="ustacks/PopA_01.snps.tsv" />
60c1c4d7d2c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
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113 <element name="PopA_01.tags" ftype="tabular" value="ustacks/PopA_01.tags.tsv" />
60c1c4d7d2c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
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114 <element name="PopA_02.alleles" ftype="tabular" value="ustacks/PopA_02.alleles.tsv" />
60c1c4d7d2c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
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115 <element name="PopA_02.snps" ftype="tabular" value="ustacks/PopA_02.snps.tsv" />
60c1c4d7d2c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
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116 <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv" />
0
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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117 </collection>
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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118 </param>
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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119 <param name="input_matches">
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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120 <collection type="list">
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121 <element name="PopA_01.matches" ftype="tabular" value="sstacks/PopA_01.matches.tsv" />
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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122 <element name="PopA_02.matches" ftype="tabular" value="sstacks/PopA_02.matches.tsv" />
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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123 </collection>
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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124 </param>
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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125 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
4
60c1c4d7d2c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
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126 <param name="input_type|input_type_select" value="single"/>
60c1c4d7d2c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
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127 <param name="input_type|fqinputs" value="demultiplexed/PopA_01.2.fq,demultiplexed/PopA_02.2.fq" ftype="fastqsanger" />
0
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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128 <param name="add_log" value="yes" />
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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129 <output name="output_log"><assert_contents><has_text text="done." /></assert_contents></output>
4
60c1c4d7d2c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
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130 <output_collection name="bams" type="list" count="2"/>
0
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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131 </test>
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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132 <!-- test w reverse reads as list -->
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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133 <test>
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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134 <param name="input_cat">
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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135 <collection type="list">
4
60c1c4d7d2c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
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diff changeset
136 <element name="catalog.alleles" ftype="tabular" value="cstacks/catalog.alleles.tsv" />
60c1c4d7d2c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
matthias
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diff changeset
137 <element name="catalog.snps" ftype="tabular" value="cstacks/catalog.snps.tsv" />
60c1c4d7d2c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
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138 <element name="catalog.tags" ftype="tabular" value="cstacks/catalog.tags.tsv" />
0
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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139 </collection>
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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140 </param>
4
60c1c4d7d2c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
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141 <param name="input_stacks">
0
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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142 <collection type="list">
4
60c1c4d7d2c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
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143 <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv" />
60c1c4d7d2c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
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144 <element name="PopA_01.snps" ftype="tabular" value="ustacks/PopA_01.snps.tsv" />
60c1c4d7d2c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
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145 <element name="PopA_01.tags" ftype="tabular" value="ustacks/PopA_01.tags.tsv" />
60c1c4d7d2c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
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diff changeset
146 <element name="PopA_02.alleles" ftype="tabular" value="ustacks/PopA_02.alleles.tsv" />
60c1c4d7d2c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
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diff changeset
147 <element name="PopA_02.snps" ftype="tabular" value="ustacks/PopA_02.snps.tsv" />
60c1c4d7d2c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
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148 <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv" />
0
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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149 </collection>
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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150 </param>
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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151 <param name="input_matches">
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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152 <collection type="list">
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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153 <element name="PopA_01.matches" ftype="tabular" value="sstacks/PopA_01.matches.tsv" />
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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154 <element name="PopA_02.matches" ftype="tabular" value="sstacks/PopA_02.matches.tsv" />
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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155 </collection>
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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156 </param>
4
60c1c4d7d2c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
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157 <param name="input_type|input_type_select" value="paired"/>
60c1c4d7d2c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
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158 <param name="input_type|fqinputs">
0
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159 <collection type="list">
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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160 <element name="PopA_01" value="demultiplexed/PopA_01.2.fq" ftype="fastqsanger" />
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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161 <element name="PopA_02" value="demultiplexed/PopA_02.2.fq" ftype="fastqsanger"/>
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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162 </collection>
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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163 </param>
99d0b19ef534 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
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164 <param name="add_log" value="yes" />
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165 <output name="output_log"><assert_contents><has_text text="done." /></assert_contents></output>
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166 <output_collection name="bams" type="list" count="2"/>
0
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167 </test>
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168 <!-- test w paired reads as paired dataset list -->
0
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169 <test>
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170 <param name="input_cat">
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171 <collection type="list">
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172 <element name="catalog.alleles" ftype="tabular" value="cstacks/catalog.alleles.tsv" />
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173 <element name="catalog.snps" ftype="tabular" value="cstacks/catalog.snps.tsv" />
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174 <element name="catalog.tags" ftype="tabular" value="cstacks/catalog.tags.tsv" />
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175 </collection>
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176 </param>
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177 <param name="input_stacks">
0
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178 <collection type="list">
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179 <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv" />
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180 <element name="PopA_01.snps" ftype="tabular" value="ustacks/PopA_01.snps.tsv" />
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181 <element name="PopA_01.tags" ftype="tabular" value="ustacks/PopA_01.tags.tsv" />
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182 <element name="PopA_02.alleles" ftype="tabular" value="ustacks/PopA_02.alleles.tsv" />
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183 <element name="PopA_02.snps" ftype="tabular" value="ustacks/PopA_02.snps.tsv" />
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184 <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv" />
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185 </collection>
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186 </param>
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187 <param name="input_matches">
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188 <collection type="list">
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189 <element name="PopA_01.matches" ftype="tabular" value="sstacks/PopA_01.matches.tsv" />
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190 <element name="PopA_02.matches" ftype="tabular" value="sstacks/PopA_02.matches.tsv" />
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191 </collection>
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192 </param>
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193 <param name="input_type|input_type_select" value="paired"/>
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194 <param name="input_type|fqinputs">
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195 <collection type="list:paired">
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196 <element name="PopA_01">
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197 <collection type="paired">
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198 <element name="forward" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger" />
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199 <element name="reverse" value="demultiplexed/PopA_01.2.fq" ftype="fastqsanger"/>
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200 </collection>
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201 </element>
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202 <element name="PopA_02">
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203 <collection type="paired">
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204 <element name="forward" value="demultiplexed/PopA_02.1.fq" ftype="fastqsanger" />
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205 <element name="reverse" value="demultiplexed/PopA_02.2.fq" ftype="fastqsanger"/>
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206 </collection>
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207 </element>
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208 </collection>
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209 </param>
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210 <param name="add_log" value="yes" />
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211 <output name="output_log"><assert_contents><has_text text="done." /></assert_contents></output>
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212 <output_collection name="bams" type="list" count="2"/>
0
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213 </test>
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214 </tests>
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215
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216 <help>
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217 <![CDATA[
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218 .. class:: infomark
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219
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220 **What it does**
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221
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222 The unique stacks program will take as input a set of short-read sequences and align them into exactly-matching stacks. Comparing the stacks it will form a set of loci and detect SNPs at each locus using a maximum likelihood framework
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223
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224 --------
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225
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226 **Input files**
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227
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228 FASTQ, FASTA
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229
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230 **Output files**
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231
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232 - XXX.tags.tsv file:
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233
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234 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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235
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236 Notes: For the tags file, each stack will start in the file with a consensus sequence for the entire stack followed by the flags for that stack. Then, each individual read that was merged into that stack will follow. The next stack will start with another consensus sequence.
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237
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238
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239 - XXX.snps.tsv file:
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240
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241 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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242
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243 Notes: If a stack has two SNPs called within it, then there will be two lines in this file listing each one.
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244
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245
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246 - XXX.alleles.tsv file:
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247
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248 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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249
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250 @STACKS_INFOS@
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251 ]]>
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252 </help>
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253 <expand macro="citation" />
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254 </tool>