Mercurial > repos > iuc > stacks2_refmap

annotate stacks_refmap.xml @ 1:e1f99efbfd81 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
author iuc
date Mon, 30 Sep 2019 13:59:21 -0400
parents 524bd85b0bec
children 6e43ea81f086
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524bd85b0bec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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1 <tool id="stacks2_refmap" name="Stacks2: reference map" profile="@PROFILE@" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@">
524bd85b0bec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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2 <description>the Stacks pipeline with a reference genome (ref_map.pl)</description>
524bd85b0bec 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>
524bd85b0bec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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5 </macros>
524bd85b0bec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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6 <expand macro="requirements"/>
524bd85b0bec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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7 <expand macro="version_cmd"/>
524bd85b0bec 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[
524bd85b0bec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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9 @FASTQ_INPUT_FUNCTIONS@
1
e1f99efbfd81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
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10 mkdir bam_inputs stacks_outputs &&
e1f99efbfd81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
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e1f99efbfd81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
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12 #if $output_log
e1f99efbfd81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
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13 ln -s '$output_log' stacks_outputs/ref_map.log &&
e1f99efbfd81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
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14 #end if
e1f99efbfd81 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
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15
0
524bd85b0bec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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16 @BAM_INPUT@
524bd85b0bec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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524bd85b0bec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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18 ref_map.pl
524bd85b0bec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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19 --samples bam_inputs
524bd85b0bec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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20 #if str($popmap) != 'None':
524bd85b0bec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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21 --popmap '$popmap'
524bd85b0bec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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22 #end if
524bd85b0bec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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23 $paired_select
524bd85b0bec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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24 -o stacks_outputs
524bd85b0bec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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25 -T \${GALAXY_SLOTS:-1}
524bd85b0bec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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26 --var-alpha $model_options.var_alpha
524bd85b0bec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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27 --gt-alpha $model_options.gt_alpha
524bd85b0bec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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28
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29 @EXTRACT_VCF@
524bd85b0bec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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30 ]]></command>
524bd85b0bec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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31
524bd85b0bec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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32 <inputs>
524bd85b0bec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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33 <expand macro="bam_input_macro"/>
524bd85b0bec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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34 <param argument="--popmap" type="data" optional="true" format="tabular,txt" label="Population map" />
524bd85b0bec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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35 <param name="paired_select" type="select" label="Paired end options" help="select single/paired for single end data or to select advanced paired end options, --unpaired: treat reverse reads as if they were forward reads; --ignore-pe-reads: ignore paired-end reads even if present in the input">
524bd85b0bec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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36 <option value="" selected="true">single/paired</option>
524bd85b0bec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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37 <option value="--unpaired" selected="true">ignore read pairing (--unpaired)</option>
524bd85b0bec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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38 <option value="--ignore-pe-reads" selected="true">ignore paired-end reads (--ignore-pe-reads)</option>
524bd85b0bec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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39 </param>
524bd85b0bec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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40 <section name="model_options" title="Variant calling options (for gstacks)" expanded="true">
524bd85b0bec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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41 <expand macro="variant_calling_options_vg" varalpha_default="0.01"/>
524bd85b0bec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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42 </section>
524bd85b0bec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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43 <expand macro="in_log"/>
524bd85b0bec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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44 </inputs>
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45 <outputs>
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46 <expand macro="out_log"/> <!-- pipeline also writes other logs? .. could be a collection -->
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47 <expand macro="gstacks_outputs_macro" tooladd="(gstacks)"/>
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48 <expand macro="populations_output_light" tooladd="(populations)"/>
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49 </outputs>
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50
524bd85b0bec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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51 <tests>
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52 <!-- bams as list -->
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53 <test>
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54 <param name="input_bam" ftype="bam" value="refmap/PopA_01.bam,refmap/PopA_02.bam"/>
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55 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
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56 <param name="add_log" value="yes" />
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57 <output ftype="txt" name="output_log"><assert_contents><has_text text="ref_map.pl is done." /></assert_contents></output>
524bd85b0bec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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58 <output_collection name="gstacks_out" type="list" count="2">
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59 <element name="catalog.calls.vcf" file="refmap/catalog.calls.vcf" ftype="vcf" lines_diff="2"/>
524bd85b0bec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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60 <element name="catalog.fa.gz" file="refmap/catalog.fa.gz" ftype="fasta.gz" compare="sim_size"/>
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61 </output_collection>
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62 <output ftype="tabular" name="out_haplotypes" value="refmap/populations.haplotypes.tsv"/>
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63 <output ftype="tabular" name="out_hapstats" value="refmap/populations.hapstats.tsv"/>
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64 <output ftype="txt" name="out_populations_log_distribs" value="refmap/populations.log.distribs"/>
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65 <output ftype="tabular" name="out_sumstats_sum" value="refmap/populations.sumstats_summary.tsv"/>
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66 <output ftype="tabular" name="out_sumstats" value="refmap/populations.sumstats.tsv"/>
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67 <output ftype="tabular" name="out_sql" value="refmap/populations.markers.tsv"/>
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68 </test>
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69 <test>
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70 <param name="input_bam" ftype="bam" value="refmap/PopA_01.bam,refmap/PopA_02.bam"/>
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71 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
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72 <param name="paired_select" value="--unpaired"/>
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73 <param name="model_options|var_alpha" value="0.1" />
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74 <param name="model_options|gt_alpha" value="0.1" />
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75 <assert_command>
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76 <has_text text="--unpaired" />
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77 <has_text text="--var-alpha 0.1" />
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78 <has_text text="--gt-alpha 0.1" />
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79 </assert_command>
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80 <param name="add_log" value="yes" />
524bd85b0bec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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81 <output ftype="txt" name="output_log"><assert_contents><has_text text="ref_map.pl is done." /></assert_contents></output>
524bd85b0bec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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82 <output_collection name="gstacks_out" type="list" count="2"/>
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83 <output ftype="tabular" name="out_haplotypes"><assert_contents><has_text text="#"/></assert_contents></output>
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84 <output ftype="tabular" name="out_hapstats"><assert_contents><has_text text="#"/></assert_contents></output>
524bd85b0bec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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85 <output ftype="txt" name="out_populations_log_distribs"><assert_contents><has_text text="#"/></assert_contents></output>
524bd85b0bec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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86 <output ftype="tabular" name="out_sumstats_sum"><assert_contents><has_text text="#"/></assert_contents></output>
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87 <output ftype="tabular" name="out_sumstats"><assert_contents><has_text text="#"/></assert_contents></output>
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88 <output ftype="tabular" name="out_sql"><assert_contents><has_text text="#"/></assert_contents></output>
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89
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90 </test>
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91 </tests>
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92
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93 <help>
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94 <![CDATA[
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95 .. class:: infomark
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96
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97 **What it does**
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98
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99 This program expects data that have been aligned to a reference genome, and can accept data directly from Bowtie, or from any aligner that can produce SAM format. To avoid datasets names problems, we recommand the use of the *Map with BWA for STACKS tool*. This program will execute each of the Stacks components: first, running pstacks on each of the samples specified, building loci (based on the reference alignment) and calling SNPs in each. Second, cstacks will be run to create a catalog of all loci specified as 'parents' or 'samples' on the command line, again using alignment to match loci in the catalog. Finally, sstacks will be executed to match each sample against the catalog. The ref_map.pl program will also load the results of each stage of the analysis: individual loci, the catalog, and matches against the catalog into the database (although this can be disabled). After matching the program will build a database index to speed up access (index_radtags.pl) and enable web-based filtering.
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100
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101 --------
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102
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103 **Input files**
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104
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105 - SAM, BAM
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106
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107 - Population map::
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108
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109 indv_01 1
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110 indv_02 1
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111 indv_03 1
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112 indv_04 2
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113 indv_05 2
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114 indv_06 2
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115
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116 **Output files**
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117
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118 - XXX.tags.tsv file:
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119
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120 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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121
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122 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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123
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124
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125 - XXX.snps.tsv file:
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126
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127 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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128
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129 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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130
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131
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132 - XXX.alleles.tsv file:
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133
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134 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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135
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136
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137 - XXX.matches.tsv file:
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138
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139 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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140
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141 Notes: Each line in this file records a match between a catalog locus and a locus in an individual, for a particular haplotype. The Batch ID plus the Catalog ID together represent a unique locus in the entire population, while the Sample ID and the Stack ID together represent a unique locus in an individual sample.
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142
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143
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144 - other files:
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145
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146 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
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147
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148 @STACKS_INFOS@
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149 ]]>
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150 </help>
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151 <expand macro="citation" />
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152 </tool>