Mercurial > repos > iuc > stacks2_tsv2bam

annotate stacks_tsv2bam.xml @ 7:2645575d1bf2 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 17:58:38 +0000
parents a4b4bd84f69e
children
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1 <tool id="stacks2_tsv2bam" name="Stacks2: tsv2bam" profile="@PROFILE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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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>
4
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6 <expand macro="requirements">
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7 <requirement type="package" version="1.13">samtools</requirement>
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8 </expand>
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9 <expand macro="version_cmd"/>
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10 <command detect_errors="aggressive"><![CDATA[
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11 @FASTQ_INPUT_FUNCTIONS@
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12
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13 mkdir stacks_inputs stacks_outputs &&
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14
1
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15 #if $output_log
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16 ln -s '$output_log' stacks_inputs/tsv2bam.log &&
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17 #end if
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18
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19 @LINK_STACKS_INPUT@
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20 @LINK_CAT_INPUT@
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21 @LINK_MATCHES_INPUT@
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23 ## link fastq files into stacks_inputs/
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24 #set $paired_reads=False
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25 #for $sample in $input_type.fqinputs:
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26 #if not $sample:
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27 #continue
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28 #end if
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29 #set $paired_reads=True
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30 #set ($link_cmd, $data_path, $name, $inputype) = $fastq_input_foo($sample, "reverse", ".2")
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31 $link_cmd
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32 #end for
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33
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34 tsv2bam
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35 -P stacks_inputs
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36 #if $popmap
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37 -M '$popmap'
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38 #else
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39 #for $sample in $samples
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40 -s '$sample'
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41 #end for
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42 #end if
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43 #if $paired_reads
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44 --pe-reads-dir stacks_inputs
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45 #end if
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46 -t \${GALAXY_SLOTS:-1}
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47 ## tsv2bam writes to stdout and creates a log file
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48 ## - make stdout stderr
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49 ## - move the additional log file
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50 2>&1
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51
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52 && mv stacks_inputs/*matches.bam stacks_outputs
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54 ## see comment in gstacks
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55 && for b in stacks_outputs/*matches.bam; do (samtools view -b "\$b" || true) 2> /dev/null > tmp && mv tmp "\$b"; done
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56 ]]></command>
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57
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58 <inputs>
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59 <expand macro="input_stacks_macro"/>
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60 <expand macro="input_cat_macro"/>
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61 <expand macro="input_matches_macro"/>
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62 <!-- TODO add BAM? -->
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63 <expand macro="fastq_input" fastq_optional="true" multiple="true" listtype="list:paired" 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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64 <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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65 <expand macro="in_log"/>
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66 </inputs>
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67
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68 <outputs>
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69 <expand macro="out_log"/>
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70 <expand macro="tsv2bam_outputs_macro"/>
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71 </outputs>
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72
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73 <tests>
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74 <!-- test wo paired end data (this is not the default used in denovomap .. which is used for generating the test data therefore we only test if a list of two bams is generated) -->
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75 <test expect_num_outputs="2">
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76 <param name="input_cat">
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77 <collection type="list">
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78 <element name="catalog.alleles" ftype="tabular" value="cstacks/catalog.alleles.tsv"/>
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79 <element name="catalog.snps" ftype="tabular" value="cstacks/catalog.snps.tsv"/>
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80 <element name="catalog.tags" ftype="tabular" value="cstacks/catalog.tags.tsv"/>
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81 </collection>
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82 </param>
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83 <param name="input_stacks">
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84 <collection type="list">
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85 <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv"/>
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86 <element name="PopA_01.snps" ftype="tabular" value="ustacks/PopA_01.snps.tsv"/>
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87 <element name="PopA_01.tags" ftype="tabular" value="ustacks/PopA_01.tags.tsv"/>
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88 <element name="PopA_02.alleles" ftype="tabular" value="ustacks/PopA_02.alleles.tsv"/>
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89 <element name="PopA_02.snps" ftype="tabular" value="ustacks/PopA_02.snps.tsv"/>
bf0e43ab0416 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
90 <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv"/>
0
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
91 </collection>
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
92 </param>
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
93 <param name="input_matches">
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
94 <collection type="list">
2
bf0e43ab0416 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
95 <element name="PopA_01.matches" ftype="tabular" value="sstacks/PopA_01.matches.tsv"/>
bf0e43ab0416 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
96 <element name="PopA_02.matches" ftype="tabular" value="sstacks/PopA_02.matches.tsv"/>
0
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
97 </collection>
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
98 </param>
2
bf0e43ab0416 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
99 <param name="add_log" value="yes"/>
0
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
100 <output name="output_log" ftype="txt" file="tsv2bam/tsv2bam.log" lines_diff="14"/>
4
69842dd5aa48 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents: 2
diff changeset
101 <output_collection name="bams" type="list" count="2"/>
69842dd5aa48 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents: 2
diff changeset
102 </test>
69842dd5aa48 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents: 2
diff changeset
103 <!-- test w popmap, w reverse reads as multiple selection -->
69842dd5aa48 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents: 2
diff changeset
104 <test expect_num_outputs="2">
69842dd5aa48 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents: 2
diff changeset
105 <param name="input_cat">
69842dd5aa48 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents: 2
diff changeset
106 <collection type="list">
69842dd5aa48 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents: 2
diff changeset
107 <element name="catalog.alleles" ftype="tabular" value="cstacks/catalog.alleles.tsv"/>
69842dd5aa48 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents: 2
diff changeset
108 <element name="catalog.snps" ftype="tabular" value="cstacks/catalog.snps.tsv"/>
69842dd5aa48 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents: 2
diff changeset
109 <element name="catalog.tags" ftype="tabular" value="cstacks/catalog.tags.tsv"/>
69842dd5aa48 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents: 2
diff changeset
110 </collection>
69842dd5aa48 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents: 2
diff changeset
111 </param>
69842dd5aa48 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents: 2
diff changeset
112 <param name="input_stacks">
69842dd5aa48 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents: 2
diff changeset
113 <collection type="list">
69842dd5aa48 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents: 2
diff changeset
114 <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv"/>
69842dd5aa48 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents: 2
diff changeset
115 <element name="PopA_01.snps" ftype="tabular" value="ustacks/PopA_01.snps.tsv"/>
69842dd5aa48 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents: 2
diff changeset
116 <element name="PopA_01.tags" ftype="tabular" value="ustacks/PopA_01.tags.tsv"/>
69842dd5aa48 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents: 2
diff changeset
117 <element name="PopA_02.alleles" ftype="tabular" value="ustacks/PopA_02.alleles.tsv"/>
69842dd5aa48 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents: 2
diff changeset
118 <element name="PopA_02.snps" ftype="tabular" value="ustacks/PopA_02.snps.tsv"/>
69842dd5aa48 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents: 2
diff changeset
119 <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv"/>
69842dd5aa48 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents: 2
diff changeset
120 </collection>
69842dd5aa48 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents: 2
diff changeset
121 </param>
69842dd5aa48 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents: 2
diff changeset
122 <param name="input_matches">
69842dd5aa48 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents: 2
diff changeset
123 <collection type="list">
69842dd5aa48 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents: 2
diff changeset
124 <element name="PopA_01.matches" ftype="tabular" value="sstacks/PopA_01.matches.tsv"/>
69842dd5aa48 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents: 2
diff changeset
125 <element name="PopA_02.matches" ftype="tabular" value="sstacks/PopA_02.matches.tsv"/>
69842dd5aa48 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents: 2
diff changeset
126 </collection>
69842dd5aa48 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents: 2
diff changeset
127 </param>
69842dd5aa48 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents: 2
diff changeset
128 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
69842dd5aa48 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents: 2
diff changeset
129 <param name="input_type|input_type_select" value="single"/>
69842dd5aa48 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents: 2
diff changeset
130 <param name="input_type|fqinputs" value="demultiplexed/PopA_01.2.fq,demultiplexed/PopA_02.2.fq" ftype="fastqsanger"/>
69842dd5aa48 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents: 2
diff changeset
131 <param name="add_log" value="yes"/>
69842dd5aa48 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents: 2
diff changeset
132 <output name="output_log"><assert_contents><has_text text="done."/></assert_contents></output>
69842dd5aa48 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
iuc
parents: 2
diff changeset
133 <output_collection name="bams" type="list" count="2"/>
0
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
134 </test>
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
135 <!-- test w popmap, w reverse reads as multiple selection -->
2
bf0e43ab0416 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
136 <test expect_num_outputs="2">
0
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
137 <param name="input_cat">
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
138 <collection type="list">
2
bf0e43ab0416 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
139 <element name="catalog.alleles" ftype="tabular" value="cstacks/catalog.alleles.tsv"/>
bf0e43ab0416 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
140 <element name="catalog.snps" ftype="tabular" value="cstacks/catalog.snps.tsv"/>
bf0e43ab0416 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
141 <element name="catalog.tags" ftype="tabular" value="cstacks/catalog.tags.tsv"/>
0
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
142 </collection>
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
143 </param>
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
144 <param name="input_stacks">
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
145 <collection type="list">
2
bf0e43ab0416 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
146 <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv"/>
bf0e43ab0416 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
147 <element name="PopA_01.snps" ftype="tabular" value="ustacks/PopA_01.snps.tsv"/>
bf0e43ab0416 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
148 <element name="PopA_01.tags" ftype="tabular" value="ustacks/PopA_01.tags.tsv"/>
bf0e43ab0416 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
149 <element name="PopA_02.alleles" ftype="tabular" value="ustacks/PopA_02.alleles.tsv"/>
bf0e43ab0416 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
150 <element name="PopA_02.snps" ftype="tabular" value="ustacks/PopA_02.snps.tsv"/>
bf0e43ab0416 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
151 <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv"/>
0
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
152 </collection>
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
153 </param>
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
154 <param name="input_matches">
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
155 <collection type="list">
2
bf0e43ab0416 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
156 <element name="PopA_01.matches" ftype="tabular" value="sstacks/PopA_01.matches.tsv"/>
bf0e43ab0416 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
157 <element name="PopA_02.matches" ftype="tabular" value="sstacks/PopA_02.matches.tsv"/>
0
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
158 </collection>
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
159 </param>
2
bf0e43ab0416 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
160 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv"/>
0
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
161 <param name="input_type|input_type_select" value="single"/>
2
bf0e43ab0416 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
162 <param name="input_type|fqinputs" value="demultiplexed/PopA_01.2.fq,demultiplexed/PopA_02.2.fq" ftype="fastqsanger"/>
bf0e43ab0416 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
163 <param name="add_log" value="yes"/>
bf0e43ab0416 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
164 <output name="output_log"><assert_contents><has_text text="done."/></assert_contents></output>
0
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
165 <output_collection name="bams" type="list" count="2"/>
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
166 </test>
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
167 <!-- test w reverse reads as list -->
2
bf0e43ab0416 "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
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
169 <param name="input_cat">
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
170 <collection type="list">
2
bf0e43ab0416 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
171 <element name="catalog.alleles" ftype="tabular" value="cstacks/catalog.alleles.tsv"/>
bf0e43ab0416 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
172 <element name="catalog.snps" ftype="tabular" value="cstacks/catalog.snps.tsv"/>
bf0e43ab0416 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
173 <element name="catalog.tags" ftype="tabular" value="cstacks/catalog.tags.tsv"/>
0
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
174 </collection>
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
175 </param>
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
176 <param name="input_stacks">
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
177 <collection type="list">
2
bf0e43ab0416 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
178 <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv"/>
bf0e43ab0416 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
179 <element name="PopA_01.snps" ftype="tabular" value="ustacks/PopA_01.snps.tsv"/>
bf0e43ab0416 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
180 <element name="PopA_01.tags" ftype="tabular" value="ustacks/PopA_01.tags.tsv"/>
bf0e43ab0416 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
181 <element name="PopA_02.alleles" ftype="tabular" value="ustacks/PopA_02.alleles.tsv"/>
bf0e43ab0416 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
182 <element name="PopA_02.snps" ftype="tabular" value="ustacks/PopA_02.snps.tsv"/>
bf0e43ab0416 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
183 <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv"/>
0
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
184 </collection>
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
185 </param>
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
186 <param name="input_matches">
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
187 <collection type="list">
2
bf0e43ab0416 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
188 <element name="PopA_01.matches" ftype="tabular" value="sstacks/PopA_01.matches.tsv"/>
bf0e43ab0416 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
189 <element name="PopA_02.matches" ftype="tabular" value="sstacks/PopA_02.matches.tsv"/>
0
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
190 </collection>
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
191 </param>
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
192 <param name="input_type|input_type_select" value="paired"/>
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
193 <param name="input_type|fqinputs">
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
194 <collection type="list">
2
bf0e43ab0416 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
195 <element name="PopA_01" value="demultiplexed/PopA_01.2.fq" ftype="fastqsanger"/>
0
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
196 <element name="PopA_02" value="demultiplexed/PopA_02.2.fq" ftype="fastqsanger"/>
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
197 </collection>
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
198 </param>
2
bf0e43ab0416 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
199 <param name="add_log" value="yes"/>
bf0e43ab0416 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
200 <output name="output_log"><assert_contents><has_text text="done."/></assert_contents></output>
0
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
201 <output_collection name="bams" type="list" count="2"/>
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
202 </test>
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
203 <!-- test w paired reads as paired dataset list -->
2
bf0e43ab0416 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
204 <test expect_num_outputs="2">
0
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
205 <param name="input_cat">
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
206 <collection type="list">
2
bf0e43ab0416 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
207 <element name="catalog.alleles" ftype="tabular" value="cstacks/catalog.alleles.tsv"/>
bf0e43ab0416 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
208 <element name="catalog.snps" ftype="tabular" value="cstacks/catalog.snps.tsv"/>
bf0e43ab0416 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
209 <element name="catalog.tags" ftype="tabular" value="cstacks/catalog.tags.tsv"/>
0
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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diff changeset
210 </collection>
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
211 </param>
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
212 <param name="input_stacks">
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
213 <collection type="list">
2
bf0e43ab0416 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
214 <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv"/>
bf0e43ab0416 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
215 <element name="PopA_01.snps" ftype="tabular" value="ustacks/PopA_01.snps.tsv"/>
bf0e43ab0416 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
216 <element name="PopA_01.tags" ftype="tabular" value="ustacks/PopA_01.tags.tsv"/>
bf0e43ab0416 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
217 <element name="PopA_02.alleles" ftype="tabular" value="ustacks/PopA_02.alleles.tsv"/>
bf0e43ab0416 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
218 <element name="PopA_02.snps" ftype="tabular" value="ustacks/PopA_02.snps.tsv"/>
bf0e43ab0416 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
219 <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv"/>
0
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
220 </collection>
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
221 </param>
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
222 <param name="input_matches">
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
223 <collection type="list">
2
bf0e43ab0416 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
224 <element name="PopA_01.matches" ftype="tabular" value="sstacks/PopA_01.matches.tsv"/>
bf0e43ab0416 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
225 <element name="PopA_02.matches" ftype="tabular" value="sstacks/PopA_02.matches.tsv"/>
0
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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diff changeset
226 </collection>
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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diff changeset
227 </param>
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
228 <param name="input_type|input_type_select" value="paired"/>
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
229 <param name="input_type|fqinputs">
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
230 <collection type="list:paired">
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
231 <element name="PopA_01">
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
232 <collection type="paired">
2
bf0e43ab0416 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
233 <element name="forward" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger"/>
0
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
234 <element name="reverse" value="demultiplexed/PopA_01.2.fq" ftype="fastqsanger"/>
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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diff changeset
235 </collection>
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
236 </element>
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
237 <element name="PopA_02">
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
238 <collection type="paired">
2
bf0e43ab0416 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
239 <element name="forward" value="demultiplexed/PopA_02.1.fq" ftype="fastqsanger"/>
0
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
240 <element name="reverse" value="demultiplexed/PopA_02.2.fq" ftype="fastqsanger"/>
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
241 </collection>
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
242 </element>
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
243 </collection>
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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244 </param>
2
bf0e43ab0416 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
245 <param name="add_log" value="yes"/>
bf0e43ab0416 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
parents: 1
diff changeset
246 <output name="output_log"><assert_contents><has_text text="done."/></assert_contents></output>
0
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
247 <output_collection name="bams" type="list" count="2"/>
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
248 </test>
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
249 </tests>
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
250
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
251 <help>
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
252 <![CDATA[
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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253 .. class:: infomark
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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diff changeset
254
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
255 **What it does**
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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diff changeset
256
1b270fc77c81 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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257 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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259 --------
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261 **Input files**
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263 FASTQ, FASTA
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265 **Output files**
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267 - XXX.tags.tsv file:
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269 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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271 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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274 - XXX.snps.tsv file:
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276 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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278 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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281 - XXX.alleles.tsv file:
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283 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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285 @STACKS_INFOS@
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286 ]]>
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287 </help>
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288 <expand macro="citation"/>
0
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289 </tool>