Mercurial > repos > iuc > stacks2_tsv2bam

annotate stacks_tsv2bam.xml @ 0:d2486dc8febe draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
author iuc
date Mon, 01 Jul 2019 10:51:06 -0400
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d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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1 <tool id="stacks2_tsv2bam" name="Stacks2: tsv2bam" profile="@PROFILE@" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@">
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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2 <description>Sort reads by RAD locus</description>
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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3 <macros>
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4 <import>macros.xml</import>
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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5 </macros>
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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6 <expand macro="requirements"/>
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7 <expand macro="version_cmd"/>
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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8 <command detect_errors="aggressive"><![CDATA[
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9 @FASTQ_INPUT_FUNCTIONS@
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10
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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11 mkdir stacks_inputs stacks_outputs &&
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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12
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13 @LINK_STACKS_INPUT@
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14 @LINK_CAT_INPUT@
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15 @LINK_MATCHES_INPUT@
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16
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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17 ## link fastq files into stacks_inputs/
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18 #set $paired_reads=False
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19 #for $sample in $input_type.fqinputs:
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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20 #if not $sample:
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21 #continue
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22 #end if
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23 #set $paired_reads=True
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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24 #set ($link_cmd, $data_path, $name, $inputype) = $fastq_input_foo($sample, "reverse", ".2")
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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25 $link_cmd
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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26 #end for
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27
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28 tsv2bam
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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29 -P stacks_inputs
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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30 #if $popmap
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31 -M '$popmap'
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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32 #else
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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33 #for $sample in $samples
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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34 -s '$sample'
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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35 #end for
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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36 #end if
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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37 #if $paired_reads
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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38 --pe-reads-dir stacks_inputs
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39 #end if
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40 -t \${GALAXY_SLOTS:-1}
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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41 ## tsv2bam writes to stdout and creates a log file
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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42 ## - make stdout stderr
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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43 ## - move the additional log file
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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44 2>&1
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45
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46 #if $output_log
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47 && mv stacks_inputs/tsv2bam.log $output_log
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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48 #end if
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49 && mv stacks_inputs/*matches.bam stacks_outputs
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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50 ]]></command>
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51
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52 <inputs>
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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53 <expand macro="input_stacks_macro"/>
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54 <expand macro="input_cat_macro"/>
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55 <expand macro="input_matches_macro"/>
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56 <!-- TODO add BAM? -->
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57 <expand macro="fastq_input" fastq_optional="true" se_option="reverse reads" help="Paired end data or reverse reads. If a paired list is provided only the reverse reads are used in tsv2bam. Leave selection empty if you analyse single end data."/>
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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58 <param name="popmap" type="data" format="tabular,txt" label="Population map" help="If set, matching will be done only for samples listed in this file" optional="true" argument="-M" />
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59 <expand macro="in_log"/>
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60 </inputs>
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61
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62 <outputs>
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63 <expand macro="out_log"/>
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64 <expand macro="tsv2bam_outputs_macro"/>
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65 </outputs>
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66
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67 <tests>
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68 <!-- test wo paired end data -->
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69 <test>
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70 <param name="input_cat">
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71 <collection type="list">
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72 <element name="catalog.alleles" ftype="tabular" value="cstacks/catalog.alleles.tsv" />
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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73 <element name="catalog.snps" ftype="tabular" value="cstacks/catalog.snps.tsv" />
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74 <element name="catalog.tags" ftype="tabular" value="cstacks/catalog.tags.tsv" />
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75 </collection>
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76 </param>
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77 <param name="input_stacks">
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78 <collection type="list">
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79 <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv" />
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80 <element name="PopA_01.snps" ftype="tabular" value="ustacks/PopA_01.snps.tsv" />
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81 <element name="PopA_01.tags" ftype="tabular" value="ustacks/PopA_01.tags.tsv" />
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82 <element name="PopA_02.alleles" ftype="tabular" value="ustacks/PopA_02.alleles.tsv" />
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83 <element name="PopA_02.snps" ftype="tabular" value="ustacks/PopA_02.snps.tsv" />
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84 <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv" />
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85 </collection>
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86 </param>
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87 <param name="input_matches">
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88 <collection type="list">
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89 <element name="PopA_01.matches" ftype="tabular" value="sstacks/PopA_01.matches.tsv" />
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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90 <element name="PopA_02.matches" ftype="tabular" value="sstacks/PopA_02.matches.tsv" />
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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91 </collection>
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iuc
parents:
diff changeset
92 </param>
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
93 <param name="add_log" value="yes" />
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
94 <output name="output_log" ftype="txt" file="tsv2bam/tsv2bam.log" lines_diff="14"/>
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
95 <output_collection name="bams" type="list" count="2">
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
96 <element name="PopA_01.matches" file="tsv2bam/PopA_01.matches.bam" ftype="bam"/>
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
97 <element name="PopA_02.matches" file="tsv2bam/PopA_02.matches.bam" ftype="bam"/>
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
98 </output_collection>
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
99 </test>
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
100 <!-- test w popmap, w reverse reads as multiple selection -->
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
101 <test>
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
102 <param name="input_cat">
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
103 <collection type="list">
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
104 <element name="catalog.alleles" ftype="tabular" value="cstacks/catalog.alleles.tsv" />
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
105 <element name="catalog.snps" ftype="tabular" value="cstacks/catalog.snps.tsv" />
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
106 <element name="catalog.tags" ftype="tabular" value="cstacks/catalog.tags.tsv" />
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
107 </collection>
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
108 </param>
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
109 <param name="input_stacks">
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
110 <collection type="list">
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
111 <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv" />
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
112 <element name="PopA_01.snps" ftype="tabular" value="ustacks/PopA_01.snps.tsv" />
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
113 <element name="PopA_01.tags" ftype="tabular" value="ustacks/PopA_01.tags.tsv" />
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
114 <element name="PopA_02.alleles" ftype="tabular" value="ustacks/PopA_02.alleles.tsv" />
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
115 <element name="PopA_02.snps" ftype="tabular" value="ustacks/PopA_02.snps.tsv" />
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
116 <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv" />
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
117 </collection>
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
118 </param>
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
119 <param name="input_matches">
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
120 <collection type="list">
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
121 <element name="PopA_01.matches" ftype="tabular" value="sstacks/PopA_01.matches.tsv" />
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
122 <element name="PopA_02.matches" ftype="tabular" value="sstacks/PopA_02.matches.tsv" />
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
123 </collection>
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
124 </param>
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
125 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
126 <param name="input_type|input_type_select" value="single"/>
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
127 <param name="input_type|fqinputs" value="demultiplexed/PopA_01.2.fq,demultiplexed/PopA_02.2.fq" ftype="fastqsanger" />
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
128 <param name="add_log" value="yes" />
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
129 <output name="output_log"><assert_contents><has_text text="done." /></assert_contents></output>
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
130 <output_collection name="bams" type="list" count="2"/>
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
131 </test>
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
132 <!-- test w reverse reads as list -->
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
133 <test>
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
134 <param name="input_cat">
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
135 <collection type="list">
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
136 <element name="catalog.alleles" ftype="tabular" value="cstacks/catalog.alleles.tsv" />
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
137 <element name="catalog.snps" ftype="tabular" value="cstacks/catalog.snps.tsv" />
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
138 <element name="catalog.tags" ftype="tabular" value="cstacks/catalog.tags.tsv" />
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
139 </collection>
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
140 </param>
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
141 <param name="input_stacks">
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
142 <collection type="list">
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
143 <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv" />
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
144 <element name="PopA_01.snps" ftype="tabular" value="ustacks/PopA_01.snps.tsv" />
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
145 <element name="PopA_01.tags" ftype="tabular" value="ustacks/PopA_01.tags.tsv" />
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
146 <element name="PopA_02.alleles" ftype="tabular" value="ustacks/PopA_02.alleles.tsv" />
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
147 <element name="PopA_02.snps" ftype="tabular" value="ustacks/PopA_02.snps.tsv" />
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
148 <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv" />
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
149 </collection>
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
150 </param>
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
151 <param name="input_matches">
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
152 <collection type="list">
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
153 <element name="PopA_01.matches" ftype="tabular" value="sstacks/PopA_01.matches.tsv" />
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
154 <element name="PopA_02.matches" ftype="tabular" value="sstacks/PopA_02.matches.tsv" />
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
155 </collection>
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
156 </param>
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
157 <param name="input_type|input_type_select" value="paired"/>
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
158 <param name="input_type|fqinputs">
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
159 <collection type="list">
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
160 <element name="PopA_01" value="demultiplexed/PopA_01.2.fq" ftype="fastqsanger" />
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
161 <element name="PopA_02" value="demultiplexed/PopA_02.2.fq" ftype="fastqsanger"/>
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
162 </collection>
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
163 </param>
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
164 <param name="add_log" value="yes" />
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
165 <output name="output_log"><assert_contents><has_text text="done." /></assert_contents></output>
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
166 <output_collection name="bams" type="list" count="2"/>
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
167 </test>
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
168 <!-- test w paired reads as paired dataset list -->
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
169 <test>
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
170 <param name="input_cat">
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
171 <collection type="list">
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
172 <element name="catalog.alleles" ftype="tabular" value="cstacks/catalog.alleles.tsv" />
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
173 <element name="catalog.snps" ftype="tabular" value="cstacks/catalog.snps.tsv" />
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
174 <element name="catalog.tags" ftype="tabular" value="cstacks/catalog.tags.tsv" />
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
175 </collection>
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
176 </param>
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
177 <param name="input_stacks">
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
178 <collection type="list">
d2486dc8febe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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179 <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv" />
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180 <element name="PopA_01.snps" ftype="tabular" value="ustacks/PopA_01.snps.tsv" />
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181 <element name="PopA_01.tags" ftype="tabular" value="ustacks/PopA_01.tags.tsv" />
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182 <element name="PopA_02.alleles" ftype="tabular" value="ustacks/PopA_02.alleles.tsv" />
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183 <element name="PopA_02.snps" ftype="tabular" value="ustacks/PopA_02.snps.tsv" />
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184 <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv" />
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185 </collection>
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186 </param>
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187 <param name="input_matches">
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188 <collection type="list">
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189 <element name="PopA_01.matches" ftype="tabular" value="sstacks/PopA_01.matches.tsv" />
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190 <element name="PopA_02.matches" ftype="tabular" value="sstacks/PopA_02.matches.tsv" />
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191 </collection>
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192 </param>
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193 <param name="input_type|input_type_select" value="paired"/>
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194 <param name="input_type|fqinputs">
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195 <collection type="list:paired">
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196 <element name="PopA_01">
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197 <collection type="paired">
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198 <element name="forward" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger" />
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199 <element name="reverse" value="demultiplexed/PopA_01.2.fq" ftype="fastqsanger"/>
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200 </collection>
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201 </element>
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202 <element name="PopA_02">
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203 <collection type="paired">
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204 <element name="forward" value="demultiplexed/PopA_02.1.fq" ftype="fastqsanger" />
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205 <element name="reverse" value="demultiplexed/PopA_02.2.fq" ftype="fastqsanger"/>
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206 </collection>
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207 </element>
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208 </collection>
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209 </param>
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210 <param name="add_log" value="yes" />
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211 <output name="output_log"><assert_contents><has_text text="done." /></assert_contents></output>
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212 <output_collection name="bams" type="list" count="2"/>
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213 </test>
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214 </tests>
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215
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216 <help>
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217 <![CDATA[
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218 .. class:: infomark
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219
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220 **What it does**
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221
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222 The unique stacks program will take as input a set of short-read sequences and align them into exactly-matching stacks. Comparing the stacks it will form a set of loci and detect SNPs at each locus using a maximum likelihood framework
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223
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224 --------
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225
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226 **Input files**
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227
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228 FASTQ, FASTA
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229
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230 **Output files**
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231
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232 - XXX.tags.tsv file:
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233
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234 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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235
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236 Notes: For the tags file, each stack will start in the file with a consensus sequence for the entire stack followed by the flags for that stack. Then, each individual read that was merged into that stack will follow. The next stack will start with another consensus sequence.
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237
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238
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239 - XXX.snps.tsv file:
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240
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241 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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242
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243 Notes: If a stack has two SNPs called within it, then there will be two lines in this file listing each one.
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244
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245
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246 - XXX.alleles.tsv file:
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247
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248 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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249
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250 @STACKS_INFOS@
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251 ]]>
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252 </help>
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253 <expand macro="citation" />
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254 </tool>