Mercurial > repos > iuc > megan_blast2rma
comparison macros.xml @ 0:fa3c3a64c993 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 2a49a6cdc1b4d37ab30eb85b8c658ccf9f5a0644"
| author | iuc |
|---|---|
| date | Wed, 24 Nov 2021 21:52:14 +0000 |
| parents | |
| children | 2f8d3924bb3b |
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| -1:000000000000 | 0:fa3c3a64c993 |
|---|---|
| 1 <macros> | |
| 2 <token name="@TOOL_VERSION@">6.21.7</token> | |
| 3 <token name="@VERSION_SUFFIX@">0</token> | |
| 4 <token name="@PROFILE@">20.09</token> | |
| 5 <xml name="bio_tools"> | |
| 6 <xrefs> | |
| 7 <xref type="bio.tools">megan</xref> | |
| 8 </xrefs> | |
| 9 </xml> | |
| 10 <xml name="requirements"> | |
| 11 <requirements> | |
| 12 <requirement type="package" version="@TOOL_VERSION@">megan</requirement> | |
| 13 </requirements> | |
| 14 </xml> | |
| 15 <macro name="input_type_cond"> | |
| 16 <conditional name="input_type_cond"> | |
| 17 <param name="input_type" type="select" label="Choose the category of the reads files to be analyzed"> | |
| 18 <option value="single" selected="true">Single dataset</option> | |
| 19 <option value="pair">Dataset pair</option> | |
| 20 <option value="paired">List of dataset pairs</option> | |
| 21 </param> | |
| 22 <when value="single"> | |
| 23 <param name="read1" type="data" format="fasta,fasta.gz,fastqsanger.gz,fastqsanger" label="Forward read file" help="This read file should be the one used by Blast to generate the Blast file below"/> | |
| 24 <param name="blast1" type="data" format="daa,blastxml,sam,tabular,txt" label="Output file of Blast on input forward read file"/> | |
| 25 </when> | |
| 26 <when value="pair"> | |
| 27 <param name="read1" type="data" format="fasta,fasta.gz,fastqsanger.gz,fastqsanger" label="Forward read file" help="This read file should be the one used by Blast to generate the Blast file below"/> | |
| 28 <param name="read2" type="data" format="fasta,fasta.gz,fastqsanger.gz,fastqsanger" label="Reverse read file" help="This read file should be the one used by Blast to generate the Blast file below"/> | |
| 29 <param argument="--pairedSuffixLength" type="integer" value="0" label="Length of name suffix used to distinguish read names" help="Use 0 if read and mate have the same name"/> | |
| 30 <param name="blast1" type="data" format="daa,blastxml,sam,tabular,txt" label="Output file of Blast on input forward read file"/> | |
| 31 <param name="blast2" type="data" format="daa,blastxml,sam,tabular,txt" label="Output file of Blast on input reverse read file"/> | |
| 32 </when> | |
| 33 <when value="paired"> | |
| 34 <param name="reads_collection" type="data_collection" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz" collection_type="paired" label="Collection of paired read files"/> | |
| 35 <param argument="--pairedSuffixLength" type="integer" value="0" label="Length of name suffix used to distinguish read names" help="Use 0 if read and mate have the same name"/> | |
| 36 <param name="blast1" type="data" format="daa,blastxml,sam,tabular,txt" label="Blast file for forward read"/> | |
| 37 <param name="blast2" type="data" format="daa,blastxml,sam,tabular,txt" label="Blast file for reverse read"/> | |
| 38 </when> | |
| 39 </conditional> | |
| 40 </macro> | |
| 41 <macro name="blast_mode_options"> | |
| 42 <option value="Unknown" selected="true">Unknown</option> | |
| 43 <option value="BlastN">BlastN</option> | |
| 44 <option value="BlastP">BlastP</option> | |
| 45 <option value="BlastX">BlastX</option> | |
| 46 <option value="Classifier">Classifier</option> | |
| 47 </macro> | |
| 48 <macro name="common_blast_params"> | |
| 49 <param argument="--minScore" type="float" value="50.0" label="Minimum score"/> | |
| 50 <param argument="--maxExpected" type="float" value="0.01" label="Maximum expected"/> | |
| 51 <param argument="--minPercentIdentity" type="float" value="0.0" min="0.0" max="100.0" label="Minimum percent identity"/> | |
| 52 <param argument="--topPercent" type="float" value="10.0" min="0.0" max="100.0" label="Top percent"/> | |
| 53 </macro> | |
| 54 <xml name="sanitize_query" token_validinitial="string.printable"> | |
| 55 <sanitizer> | |
| 56 <valid initial="@VALIDINITIAL@"> | |
| 57 <remove value="'" /> | |
| 58 <add value="|" /> | |
| 59 </valid> | |
| 60 <mapping initial="none"> | |
| 61 <add source="'" target="'"'"'" /> | |
| 62 </mapping> | |
| 63 </sanitizer> | |
| 64 </xml> | |
| 65 <xml name="citations"> | |
| 66 <citations> | |
| 67 <citation type="doi">10.1101/gr.5969107</citation> | |
| 68 </citations> | |
| 69 </xml> | |
| 70 </macros> | |
| 71 |