Mercurial > repos > iuc > stacks2_ustacks

annotate stacks_ustacks.xml @ 7:5c478d56c19e draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit feda4e2ea70c013fcddd1dbdeab73158fe9c86a4
author iuc
date Mon, 23 May 2022 17:41:56 +0000
parents cee1b75beeaf
children
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6df4c5bf0a91 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
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1 <tool id="stacks2_ustacks" name="Stacks2: ustacks" profile="@PROFILE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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2 <description>Identify unique stacks</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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10
2
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11 trap ">&2 cat '$output_log'" err exit &&
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12 mkdir stacks_inputs stacks_outputs &&
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14 #set $ID=int($processing_options.i)
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15 #for $sample in $input_type.fqinputs
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16 #set ($create_links, $data_path, $name, $inputype) = $fastq_input_foo($sample, "forward", ".1")
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17 $create_links
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19 ustacks
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21 -f '$data_path'
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22 -i $ID
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23 --name $name
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24 -m $m
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25 -M $M
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26 #if $N
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27 -N $N
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28 #end if
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29 -p \${GALAXY_SLOTS:-1}
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30 -t $inputype
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31 $R
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32 $H
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33
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34 ## Assembly
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35 $assembly_options.keep_high_cov
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36 --high_cov_thres $assembly_options.high_cov_thres
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37 $assembly_options.d
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38 --max_locus_stacks $assembly_options.max_locus_stacks
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39 #if str($assembly_options.k_len)
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40 --k_len $assembly_options.k_len
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41 #end if
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43 @GAP_OPTIONS@
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44
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45 ## snp_model
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46 #if str( $snp_options.select_model.model_type) == "bounded"
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47 --model_type bounded
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48 --bound_low $snp_options.select_model.bound_low
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49 --bound_high $snp_options.select_model.bound_high
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50 --alpha $snp_options.select_model.alpha
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51 #else if str( $snp_options.select_model.model_type) == "snp"
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52 --model_type snp
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53 --alpha $snp_options.select_model.alpha
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54 #else
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55 --model_type fixed
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56 --bc_err_freq $bc_err_freq
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57 #end if
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58
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59 -o stacks_outputs
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60 @TEE_APPEND_LOG@
2
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61 &&
0
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62
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63 #set $ID=$ID+1
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64 #end for
2
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65 true
0
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66 ## If input is in gz format, stacks will output gzipped files (no option to control this)
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67 #if $inputype.startswith('gz')
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68 && gunzip stacks_outputs/*.gz
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69 #end if
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70 ]]></command>
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71
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72 <inputs>
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73 <expand macro="fastq_input" multiple="true" listtype="list:paired" help="Single end data or forward reads. If a paired list is provided only the forward reads are used in ustacks"/>
0
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74
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75 <param argument="-m" type="integer" value="3" label="Minimum depth of coverage required to create a stack"/>
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76 <param argument="-M" type="integer" value="2" label="Maximum distance (in nucleotides) allowed between stacks"/>
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77 <param argument="-N" type="integer" value="" optional="true" label="Maximum distance allowed to align secondary reads to primary stacks" help="(default: M + 2)"/>
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78 <param argument="-R" type="boolean" checked="false" truevalue="-R" falsevalue="" label="Retain unused reads"/>
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79 <param argument="-H" type="boolean" checked="false" truevalue="-H" falsevalue="" label="Disable calling haplotypes from secondary reads"/>
0
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80 <section name="assembly_options" title="SNP Model Options (ustacks options)" expanded="True">
2
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81 <param argument="--keep_high_cov" type="boolean" checked="false" truevalue="--keep_high_cov" falsevalue="" label="Disable the algorithm that removes highly-repetitive stacks and nearby errors. "/>
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82 <param argument="-d" type="boolean" checked="false" truevalue="-d" falsevalue="" label="Enable the Deleveraging algorithm, used for resolving over merged tags"/>
0
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83 <param argument="--high_cov_thres" type="float" min="0.0" value="3.0" label="Highly-repetitive stacks threshold" help="in standard deviation units"/>
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84 <param argument="--max_locus_stacks" type="integer" value="3" label="Maximum number of stacks at a single de novo locus"/>
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85 <param argument="--k_len" type="integer" value="" min="7" max="31" optional="true" label="K-mer size for matching between alleles and loci (automatically calculated by default)"/>
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86 </section>
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87 <expand macro="gap_options"/>
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88
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89 <!-- SNP Model options -->
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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90 <section name="snp_options" title="SNP Model Options (ustacks options)" expanded="False">
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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91 <expand macro="snp_options_full"/>
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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92 </section>
6
cee1b75beeaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
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93 <section name="processing_options" title="Processing options" expanded="False">
cee1b75beeaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
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94 <param argument="-i" type="integer" value="1" label="Start identifier at" help="If you are combining multiple ustacks runs at the cstacks stage, use this option to avoid having different samples with the same identifier."/>
cee1b75beeaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
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95 </section>
0
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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96 <expand macro="in_log"/>
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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97 </inputs>
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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98
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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99 <outputs>
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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100 <expand macro="out_log"/>
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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101 <expand macro="ustacks_outputs_macro"/>
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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102 </outputs>
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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103
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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104 <tests>
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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105 <!-- paired list, default options, test for file equality -->
2
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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parents: 1
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106 <test expect_num_outputs="2">
0
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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107 <param name="input_type|input_type_select" value="paired"/>
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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108 <param name="input_type|fqinputs">
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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109 <collection type="list:paired">
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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110 <element name="PopA_01">
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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111 <collection type="paired">
2
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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parents: 1
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112 <element name="forward" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger"/>
0
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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113 <element name="reverse" value="demultiplexed/PopA_01.2.fq" ftype="fastqsanger"/>
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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114 </collection>
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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115 </element>
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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116 <element name="PopA_02">
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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117 <collection type="paired">
2
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
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118 <element name="forward" value="demultiplexed/PopA_02.1.fq" ftype="fastqsanger"/>
0
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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119 <element name="reverse" value="demultiplexed/PopA_02.2.fq" ftype="fastqsanger"/>
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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120 </collection>
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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diff changeset
121 </element>
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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diff changeset
122 </collection>
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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123 </param>
2
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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124 <param name="add_log" value="yes"/>
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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125 <output name="output_log"><assert_contents><has_text text="done."/></assert_contents></output>
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
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126 <!-- 1st test checks for file content allowing differences in the 2 comment lines that contain date and version -->
0
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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127 <output_collection name="tabs" type="list" count="6">
6
cee1b75beeaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
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diff changeset
128 <element name="PopA_01.tags">
cee1b75beeaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
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129 <assert_contents>
cee1b75beeaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
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130 <has_text text="# ustacks version" />
cee1b75beeaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
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131 </assert_contents>
cee1b75beeaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
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diff changeset
132 </element>
cee1b75beeaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
133 <element name="PopA_01.snps">
cee1b75beeaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
134 <assert_contents>
cee1b75beeaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
135 <has_text text="# ustacks version" />
cee1b75beeaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
136 </assert_contents>
cee1b75beeaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
137 </element>
cee1b75beeaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
138 <expand macro="test_element_stacks_completed" element_name="PopA_01.alleles" />
cee1b75beeaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
139 <element name="PopA_02.tags">
cee1b75beeaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
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diff changeset
140 <assert_contents>
cee1b75beeaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
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diff changeset
141 <has_text text="# ustacks version" />
cee1b75beeaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
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142 </assert_contents>
cee1b75beeaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
143 </element>
cee1b75beeaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
144 <element name="PopA_02.snps">
cee1b75beeaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
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diff changeset
145 <assert_contents>
cee1b75beeaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
146 <has_text text="# ustacks version" />
cee1b75beeaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
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diff changeset
147 </assert_contents>
cee1b75beeaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
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diff changeset
148 </element>
cee1b75beeaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
149 <expand macro="test_element_stacks_completed" element_name="PopA_02.alleles" />
0
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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150 </output_collection>
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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diff changeset
151 </test>
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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diff changeset
152 <!-- manual selected list of elements + default args, test for file equality -->
2
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
153 <test expect_num_outputs="2">
0
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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154 <param name="input_type|input_type_select" value="single"/>
2
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
155 <param name="input_type|fqinputs" value="demultiplexed/PopA_01.1.fq,demultiplexed/PopA_02.1.fq" ftype="fastqsanger"/>
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
156 <param name="add_log" value="yes"/>
0
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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diff changeset
157 <output name="output_log" ftype="txt"><assert_contents><has_text text="ustacks is done."/></assert_contents></output>
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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diff changeset
158 <output_collection name="tabs" count="6">
6
cee1b75beeaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
159 <expand macro="test_element_stacks_completed" element_name="PopA_01.tags" />
cee1b75beeaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
160 <expand macro="test_element_stacks_completed" element_name="PopA_01.snps" />
cee1b75beeaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
161 <expand macro="test_element_stacks_completed" element_name="PopA_01.alleles" />
cee1b75beeaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
162 <expand macro="test_element_stacks_completed" element_name="PopA_02.tags" />
cee1b75beeaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
163 <expand macro="test_element_stacks_completed" element_name="PopA_02.snps" />
cee1b75beeaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
parents: 5
diff changeset
164 <expand macro="test_element_stacks_completed" element_name="PopA_02.alleles" />
0
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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diff changeset
165 </output_collection>
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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diff changeset
166 </test>
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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diff changeset
167 <!-- manual selected list of elements + non-default short args, test for file presence -->
2
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
168 <test expect_num_outputs="2">
0
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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diff changeset
169 <param name="input_type|input_type_select" value="single"/>
2
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
170 <param name="input_type|fqinputs" value="demultiplexed/PopA_01.1.fq,demultiplexed/PopA_02.1.fq" ftype="fastqsanger"/>
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
171 <param name="m" value="2"/>
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
172 <param name="M" value="3"/>
1
aa646fe5a0b4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
iuc
parents: 0
diff changeset
173 <param name="N" value="4"/>
2
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
174 <param name="R" value="-R"/>
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
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175 <param name="H" value="-H"/>
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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176 <param name="add_log" value="yes"/>
0
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177 <assert_command>
2
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178 <has_text text="-m 2"/>
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179 <has_text text="-M 3"/>
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180 <has_text text="-N 4"/>
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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181 <has_text text="-R"/>
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
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182 <has_text text="-H"/>
0
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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183 </assert_command>
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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184 <output name="output_log" ftype="txt"><assert_contents><has_text text="ustacks is done."/></assert_contents></output>
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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185 <output_collection name="tabs" count="6">
6
cee1b75beeaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
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186 <expand macro="test_element_stacks_completed" element_name="PopA_01.tags" />
cee1b75beeaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
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187 <expand macro="test_element_stacks_completed" element_name="PopA_01.snps" />
cee1b75beeaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
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188 <expand macro="test_element_stacks_completed" element_name="PopA_01.alleles" />
cee1b75beeaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
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189 <expand macro="test_element_stacks_completed" element_name="PopA_02.tags" />
cee1b75beeaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
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190 <expand macro="test_element_stacks_completed" element_name="PopA_02.snps" />
cee1b75beeaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
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191 <expand macro="test_element_stacks_completed" element_name="PopA_02.alleles" />
0
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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192 </output_collection>
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193 </test>
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194 <!-- paired list, non-default model options, disabled gapped alignment, test for file presence -->
2
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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195 <test expect_num_outputs="2">
0
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196 <param name="input_type|input_type_select" value="paired"/>
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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197 <param name="input_type|fqinputs">
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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198 <collection type="list:paired">
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199 <element name="PopA_01">
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200 <collection type="paired">
2
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
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201 <element name="forward" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger"/>
0
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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202 <element name="reverse" value="demultiplexed/PopA_01.2.fq" ftype="fastqsanger"/>
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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203 </collection>
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204 </element>
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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205 <element name="PopA_02">
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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206 <collection type="paired">
2
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
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207 <element name="forward" value="demultiplexed/PopA_02.1.fq" ftype="fastqsanger"/>
0
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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208 <element name="reverse" value="demultiplexed/PopA_02.2.fq" ftype="fastqsanger"/>
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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209 </collection>
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210 </element>
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211 </collection>
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212 </param>
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213 <conditional name="select_model">
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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214 <param name="model_type" value="snp"/>
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215 <param name="alpha" value="0.1"/>
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216 <param name="bound_low" value="0.1"/>
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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217 <param name="bound_high" value="0.5"/>
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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218 <param name="bc_err_freq" value="0.1"/>
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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219 </conditional>
2
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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220 <param name="gapped|use_gapped" value="no"/>
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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221 <param name="add_log" value="yes"/>
0
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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222 <assert_command>
2
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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223 <has_text text="--model_type snp"/>
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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224 <has_text text="--alpha 0.1"/>
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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225 <not_has_text text="--bound_low 0.1"/>
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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226 <not_has_text text="--bound_high 0.5"/>
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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227 <not_has_text text="--bc_err_freq 0.1"/>
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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228 <has_text text="--disable-gapped"/>
0
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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229 </assert_command>
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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230 <output name="output_log" ftype="txt"><assert_contents><has_text text="ustacks is done."/></assert_contents></output>
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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231 <output_collection name="tabs" count="6">
6
cee1b75beeaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
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232 <expand macro="test_element_stacks_completed" element_name="PopA_01.tags" />
cee1b75beeaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
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233 <expand macro="test_element_stacks_completed" element_name="PopA_01.snps" />
cee1b75beeaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
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234 <expand macro="test_element_stacks_completed" element_name="PopA_01.alleles" />
cee1b75beeaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
iuc
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235 <expand macro="test_element_stacks_completed" element_name="PopA_02.tags" />
cee1b75beeaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
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236 <expand macro="test_element_stacks_completed" element_name="PopA_02.snps" />
cee1b75beeaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
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237 <expand macro="test_element_stacks_completed" element_name="PopA_02.alleles" />
0
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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238 </output_collection>
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239 </test>
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240 <!-- list of fwd reads, nondefault assembly and gapped alignment options, test for file presence -->
2
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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241 <test expect_num_outputs="2">
0
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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242 <param name="input_type|input_type_select" value="paired"/>
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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243 <param name="input_type|fqinputs">
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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244 <collection type="list">
2
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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245 <element name="PopA_01" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger"/>
0
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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246 <element name="PopA_02" value="demultiplexed/PopA_02.1.fq" ftype="fastqsanger"/>
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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247 </collection>
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248 </param>
1
aa646fe5a0b4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
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249 <param name="assembly_options|keep_high_cov" value="true"/>
2
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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250 <param name="assembly_options|d" value="-d"/>
0
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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251 <param name="assembly_options|high_cov_thres" value="2.0"/>
2
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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252 <param name="assembly_options|max_locus_stacks" value="4"/>
0
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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253 <param name="assembly_options|k_len" value="12"/>
2
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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254 <param name="gapped|use_gapped" value="yes"/>
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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255 <param name="gapped|max_gaps" value="3"/>
0
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256 <param name="gapped|min_aln_len" value="0.7"/>
2
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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diff changeset
257 <param name="add_log" value="yes"/>
0
9eaeea3fb1bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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258 <assert_command>
2
1dce9f3949c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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259 <has_text text="--keep_high_cov"/>
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260 <has_text text="-d"/>
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261 <has_text text="--high_cov_thres 2.0"/>
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262 <has_text text="--max_locus_stacks 4"/>
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263 <has_text text="--k_len 12"/>
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264 <has_text text="--max_gaps 3"/>
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265 <has_text text="--min_aln_len 0.7"/>
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266 </assert_command>
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267 <output name="output_log" ftype="txt"><assert_contents><has_text text="ustacks is done."/></assert_contents></output>
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268 <output_collection name="tabs" count="6">
6
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269 <expand macro="test_element_stacks_completed" element_name="PopA_01.tags" />
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270 <expand macro="test_element_stacks_completed" element_name="PopA_01.snps" />
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271 <expand macro="test_element_stacks_completed" element_name="PopA_01.alleles" />
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272 <expand macro="test_element_stacks_completed" element_name="PopA_02.tags" />
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273 <expand macro="test_element_stacks_completed" element_name="PopA_02.snps" />
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274 <expand macro="test_element_stacks_completed" element_name="PopA_02.alleles" />
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275 </output_collection>
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276 </test>
6
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277 <!-- test setting i -->
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278 <test expect_num_outputs="2">
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279 <param name="input_type|input_type_select" value="single"/>
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280 <param name="input_type|fqinputs" value="demultiplexed/PopA_01.1.fq,demultiplexed/PopA_02.1.fq" ftype="fastqsanger"/>
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281 <param name="add_log" value="yes"/>
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282 <param name="i" value="42"/>
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283 <output name="output_log" ftype="txt"><assert_contents><has_text text="ustacks is done."/></assert_contents></output>
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284 <output_collection name="tabs" count="6">
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285 <expand macro="test_element_stacks_completed" element_name="PopA_01.tags" />
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286 <expand macro="test_element_stacks_completed" element_name="PopA_01.snps" />
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287 <expand macro="test_element_stacks_completed" element_name="PopA_01.alleles" />
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288 <expand macro="test_element_stacks_completed" element_name="PopA_02.tags" />
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289 <expand macro="test_element_stacks_completed" element_name="PopA_02.snps" />
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290 <expand macro="test_element_stacks_completed" element_name="PopA_02.alleles" />
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291 </output_collection>
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292 </test>
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293
0
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294 </tests>
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295
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296 <help>
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297 <![CDATA[
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298 .. class:: infomark
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299
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300 **What it does**
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301
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302 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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303
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304 --------
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305
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306 **Input files**
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307
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308 One or more FASTQ, FASTA files. Can be given by selecting them manually, as dataset list, or paired dataset list. Note, for the latter ustacks only uses the forward reads -- reverse reads are incorporated in tsv2bam.
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309
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310 **Output files**
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311
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312 - XXX.tags.tsv file:
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313
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314 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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315
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316 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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317
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318
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319 - XXX.snps.tsv file:
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320
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321 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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322
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323 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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324
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325
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326 - XXX.alleles.tsv file:
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327
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328 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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329
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330 @STACKS_INFOS@
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331 ]]>
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332 </help>
2
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333 <expand macro="citation"/>
0
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334 </tool>