Mercurial > repos > iuc > prestor_abseq3

annotate prestor_abseq3.xml @ 6:2fe7327db816 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 1beb51cefbe9e6edc8930c7ae0421f28e7bb93c8
author iuc
date Fri, 04 Oct 2024 09:01:04 +0000
parents 9ada370c9d68
children
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9ada370c9d68 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit d52e3c9c53dd358e14e65a3a083e7d5c102f8697"
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1 <tool id="prestor_abseq3" name="pRESTOr AbSeq3 Report" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>Create HTML QC report from pRESTO outputs</description>
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3 <macros>
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4 <import>presto_macros.xml</import>
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5 </macros>
6
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6 <expand macro="bio_tools"/>
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7 <requirements>
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8 <requirement type="package" version="0.0.5">r-prestor</requirement>
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9 </requirements>
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11 <command detect_errors="exit_code"><![CDATA[
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12 ln -s '$qual1' ./quality-1_table.tab &&
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13 ln -s '$qual2' ./quality-2_table.tab &&
87ae065762f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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14 ln -s '$primer1' ./primers-1_table.tab &&
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15 ln -s '$primer2' ./primers-2_table.tab &&
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16 ln -s '$cons1' ./consensus-1_table.tab &&
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17 ln -s '$cons2' ./consensus-2_table.tab &&
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18 ln -s '$assemble' ./assemble_table.tab &&
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19 ln -s '$maskqual' ./maskqual_table.tab &&
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20 ln -s '$cregion' ./cregion_table.tab &&
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21 Rscript '${prestor_script}'
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22 ]]></command>
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24 <configfiles>
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25 <configfile name="prestor_script"><![CDATA[
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26 library(prestor)
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27 report_abseq3('.', sample='${sample}', output_dir='.', output_file='report.html', format='html')
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28 ]]>
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29 </configfile>
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30 </configfiles>
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32 <inputs>
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33 <param name="sample" type="text" label="Sample Name" help="Sample Name. Must not contain spaces.">
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34 <validator type="regex" message="Value may include alphanumeric characters, underscores and spaces.">[^\s]+</validator>
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35 </param>
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36 <param name="qual1" type="data" format="txt" label="ParseLog of FilterSeq(R1)" help="Output of running ParseLog on the log file from FilterSeq on Read 1."/>
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37 <param name="qual2" type="data" format="txt" label="ParseLog of FilterSeq(R2)" help="Output of running ParseLog on the log file from FilterSeq on Read 2."/>
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38 <param name="primer1" type="data" format="txt" label="ParseLog of MaskPrimers(R1)" help="Output of running ParseLog on the log file from MaskPrimers on Read 1."/>
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39 <param name="primer2" type="data" format="txt" label="ParseLog of MaskPrimers(R2)" help="Output of running ParseLog on the log file from MaskPrimers on Read 2."/>
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40 <param name="cons1" type="data" format="txt" label="ParseLog of BuildConsensus(R1)" help="Output of running ParseLog on the log file from BuildConsensus on Read 1."/>
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41 <param name="cons2" type="data" format="txt" label="ParseLog of BuildConsensus(R2)" help="Output of running ParseLog on the log file from BuildConsensus on Read 2."/>
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42 <param name="assemble" type="data" format="txt" label="ParseLog of AssemblePairs" help="Output of running ParseLog on the log file from AssemblePairs."/>
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43 <param name="maskqual" type="data" format="txt" label="ParseLog of FilterSeq(pairs)" help="Output of running ParseLog on the log file from FilterSeq on the consensus reads."/>
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44 <param name="cregion" type="data" format="txt" label="ParseLog of MaskPrimers(pairs)" help="Output of running ParseLog on the log file from MaskPrimers for the C Region."/>
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45 </inputs>
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46
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47 <outputs>
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48 <data name="output" format="html" from_work_dir="report.html"/>
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49 </outputs>
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50
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51 <tests>
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52 <test>
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53 <param name="sample" value="TestSample"/>
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54 <param name="qual1" value="prestor_logs/quality-1_table.tab"/>
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55 <param name="qual2" value="prestor_logs/quality-2_table.tab"/>
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56 <param name="primer1" value="prestor_logs/primers-1_table.tab"/>
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57 <param name="primer2" value="prestor_logs/primers-2_table.tab"/>
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58 <param name="cons1" value="prestor_logs/consensus-1_table.tab"/>
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59 <param name="cons2" value="prestor_logs/consensus-2_table.tab"/>
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60 <param name="assemble" value="prestor_logs/assemble_table.tab"/>
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61 <param name="maskqual" value="prestor_logs/maskqual_table.tab"/>
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62 <param name="cregion" value="prestor_logs/cregion_table.tab"/>
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63 <output name="output">
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64 <assert_contents>
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65 <has_text text="pRESTO Report"/>
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66 </assert_contents>
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67 </output>
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68 </test>
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69 </tests>
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70
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71 <help><![CDATA[
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72 Creates an HTML QC report from the log files generated when running pRESTO.
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73
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74 ]]></help>
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75
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76 <expand macro="citations" />
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77 </tool>