Mercurial > repos > iuc > stacks_stats

annotate stacks_stats.xml @ 4:2932dbe56135 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 74ee33c6e30744a6da8deb7116d431d80ee80edb
author iuc
date Fri, 07 Apr 2023 21:57:41 +0000
parents 7c23b1406c41
children
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072a0329a18e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
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1 <tool id="stacks_stats" name="Stacks: statistics" version="@WRAPPER_VERSION@.0">
072a0329a18e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
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2 <description>on stacks found for multiple samples</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="bio_tools"/>
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7 <expand macro="requirements"/>
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8 <expand macro="stdio"/>
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9 <command><![CDATA[
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10 mkdir stacks_inputs
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12 &&
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14 #for $input_file in $input_col
072a0329a18e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
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15 #set $ext = ""
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16 #if not str($input_file.element_identifier).endswith('.tsv')
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17 #set $ext = ".tsv"
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18 #end if
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19 ln -s '${input_file}' 'stacks_inputs/${input_file.element_identifier}${ext}' &&
072a0329a18e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
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20 #end for
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22 stacks_summary.py --stacks-prog '$program' --res-dir stacks_inputs --logfile '$logfile' --summary summary.html
072a0329a18e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
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23 ]]></command>
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25 <inputs>
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27 <param name="program" type="select" argument="--stacks-prog" label="Program which generated the stacks">
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28 <option value="ustacks">ustacks (denovo)</option>
072a0329a18e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
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29 <option value="pstacks">pstacks (refmap)</option>
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30 </param>
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31
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32 <param argument="--logfile" format="txt" type="data" label="Log generated by the program" />
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34 <param name="input_col" format="tabular,txt" type="data_collection" collection_type="list" label="Output from ustacks or pstacks" />
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35 </inputs>
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37 <outputs>
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38 <data format="html" name="output_summary" label="Summary from ${tool.name} on ${on_string}" from_work_dir="summary.html" />
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39 </outputs>
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41 <tests>
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42 <test>
072a0329a18e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
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43 <param name="program" value="ustacks"/>
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44 <param name="logfile" ftype="txt" value="ustacks/ustacks.out"/>
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45 <param name="input_col">
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46 <collection type="list">
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47 <element name="batch_1.catalog.alleles.tsv" ftype="tabular" value="genotypes/batch_1.catalog.alleles.tsv" />
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48 <element name="batch_1.catalog.snps.tsv" ftype="tabular" value="genotypes/batch_1.catalog.snps.tsv" />
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49 <element name="batch_1.catalog.tags.tsv" ftype="tabular" value="genotypes/batch_1.catalog.tags.tsv" />
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50 <element name="PopA_01.alleles.tsv" ftype="tabular" value="genotypes/PopA_01.alleles.tsv" />
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51 <element name="PopA_01.matches.tsv" ftype="tabular" value="genotypes/PopA_01.matches.tsv" />
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52 <element name="PopA_01.snps.tsv" ftype="tabular" value="genotypes/PopA_01.snps.tsv" />
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53 <element name="PopA_01.tags.tsv" ftype="tabular" value="genotypes/PopA_01.tags.tsv" />
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54 <element name="PopA_02.alleles.tsv" ftype="tabular" value="genotypes/PopA_02.alleles.tsv" />
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55 <element name="PopA_02.matches.tsv" ftype="tabular" value="genotypes/PopA_02.matches.tsv" />
072a0329a18e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
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56 <element name="PopA_02.snps.tsv" ftype="tabular" value="genotypes/PopA_02.snps.tsv" />
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57 <element name="PopA_02.tags.tsv" ftype="tabular" value="genotypes/PopA_02.tags.tsv" />
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58 </collection>
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59 </param>
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61 <output name="output_summary">
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62 <assert_contents>
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63 <has_text text="Stacks Statistics" />
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64 </assert_contents>
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65 </output>
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66 </test>
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67 </tests>
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68
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69 <help>
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70 <![CDATA[
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71 .. class:: infomark
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73 **What it does**
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74
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75 When given the output of ustacks or pstacks, this will generate a report containing various statistics about the detected stacks in a set of samples.
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76
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77 @STACKS_INFOS@
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78 ]]>
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79 </help>
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80 <expand macro="citation" />
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81 </tool>