Mercurial > repos > iuc > prestor_abseq3

annotate prestor_abseq3.xml @ 3:967b96c6005a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 19e832988729a92be5426131fc6114e1f7237982"
author iuc
date Fri, 02 Jul 2021 15:29:29 +0000
parents dfd01596503e
children faba8f53524e
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967b96c6005a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 19e832988729a92be5426131fc6114e1f7237982"
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1 <tool id="prestor_abseq3" name="pRESTOr AbSeq3 Report" version="@TOOL_VERSION@+galaxy1">
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2 <description>Create HTML QC report from pRESTO outputs</description>
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4 <macros>
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5 <import>presto_macros.xml</import>
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6 </macros>
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8 <requirements>
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9 <requirement type="package" version="0.0.5">r-prestor</requirement>
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10 </requirements>
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12 <command detect_errors="exit_code"><![CDATA[
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13 ln -s '$qual1' ./quality-1_table.tab &&
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14 ln -s '$qual2' ./quality-2_table.tab &&
ef917c03493c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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15 ln -s '$primer1' ./primers-1_table.tab &&
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16 ln -s '$primer2' ./primers-2_table.tab &&
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17 ln -s '$cons1' ./consensus-1_table.tab &&
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18 ln -s '$cons2' ./consensus-2_table.tab &&
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19 ln -s '$assemble' ./assemble_table.tab &&
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20 ln -s '$maskqual' ./maskqual_table.tab &&
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21 ln -s '$cregion' ./cregion_table.tab &&
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22 Rscript '${prestor_script}'
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23 ]]></command>
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24
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25 <configfiles>
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26 <configfile name="prestor_script"><![CDATA[
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27 library(prestor)
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28 report_abseq3('.', sample='${sample}', output_dir='.', output_file='report.html', format='html')
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29 ]]>
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30 </configfile>
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31 </configfiles>
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33 <inputs>
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34 <param name="sample" type="text" label="Sample Name" help="Sample Name. Must not contain spaces.">
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35 <validator type="regex" message="Value may include alphanumeric characters, underscores and spaces.">[^\s]+</validator>
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36 </param>
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37 <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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38 <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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39 <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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40 <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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41 <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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42 <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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43 <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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44 <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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45 <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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46 </inputs>
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47
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48 <outputs>
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49 <data name="output" format="html" from_work_dir="report.html"/>
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50 </outputs>
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51
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52 <tests>
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53 <test>
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54 <param name="sample" value="TestSample"/>
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55 <param name="qual1" value="prestor_logs/quality-1_table.tab"/>
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56 <param name="qual2" value="prestor_logs/quality-2_table.tab"/>
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57 <param name="primer1" value="prestor_logs/primers-1_table.tab"/>
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58 <param name="primer2" value="prestor_logs/primers-2_table.tab"/>
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59 <param name="cons1" value="prestor_logs/consensus-1_table.tab"/>
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60 <param name="cons2" value="prestor_logs/consensus-2_table.tab"/>
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61 <param name="assemble" value="prestor_logs/assemble_table.tab"/>
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62 <param name="maskqual" value="prestor_logs/maskqual_table.tab"/>
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63 <param name="cregion" value="prestor_logs/cregion_table.tab"/>
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64 <output name="output">
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65 <assert_contents>
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66 <has_text text="pRESTO Report"/>
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67 </assert_contents>
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68 </output>
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69 </test>
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70 </tests>
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71
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72 <help><![CDATA[
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73 Creates an HTML QC report from the log files generated when running pRESTO.
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74
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75 ]]></help>
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76
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77 <expand macro="citations" />
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78 </tool>