Mercurial > repos > petr-novak > repeatexplorer2
diff repex_tarean.xml @ 2:09747b55badb draft
Uploaded
author | petr-novak |
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date | Tue, 21 Apr 2020 06:39:40 -0400 |
parents | 2f52966cbaf1 |
children | f99da6158dae |
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--- a/repex_tarean.xml Mon Feb 03 02:33:59 2020 -0500 +++ b/repex_tarean.xml Tue Apr 21 06:39:40 2020 -0400 @@ -1,4 +1,4 @@ -<tool id="tarean" name="Tandem Repeat Analyzer" version="2.3.7" > +<tool id="tarean" name="Tandem Repeat Analyzer" version="2.3.8" > <stdio> <regex match="Traceback" source="stderr" level="fatal" description="Unknown error" /> <regex match="error" source="stderr" level="fatal" description="Unknown error" /> @@ -10,7 +10,7 @@ <requirement type="package">imagemagick</requirement> <requirement type="package">mafft</requirement> <requirement type="package">blast</requirement> - <requirement type="package">diamond</requirement> + <requirement type="package" version="0.9.29">diamond</requirement> <requirement type="package">blast-legacy</requirement> <requirement type="package">r-igraph</requirement> <requirement type="package">r-data.tree</requirement> @@ -28,14 +28,14 @@ <requirement type="package">r-rsqlite</requirement> <requirement type="package">r-rserve</requirement> <requirement type="package">bioconductor-biostrings</requirement> - <requirement type="package" version="2.3.7">repex_tarean</requirement> + <requirement type="package" version="2.3.8">repex_tarean</requirement> <requirement type="set_environment">REPEX</requirement> <requirement type="set_environment">REPEX_VERSION</requirement> <requirement type="package" version="0.9.1">pyrserve</requirement> </requirements> <command detect_errors="exit_code"> export PYTHONHASHSEED=0; - \${REPEX}/seqclust --paired --sample ${sample} --output_dir=tarean_output --logfile=${log} --cleanup --tarean_mode + \${REPEX}/seqclust --paired --sample ${read_sampling.sample} --output_dir=tarean_output --logfile=${log} --cleanup --tarean_mode #if $advanced_options.advanced: --mincl $advanced_options.size_threshold $advanced_options.keep_names $advanced_options.automatic_filtering -M $advanced_options.merging #if $advanced_options.custom_library.options_custom_library : @@ -75,7 +75,18 @@ <inputs> <param name="FastaFile" label="Paired-end Illumina reads" type="data" format="fasta" help="Input file must contain FASTA-formatted interlaced read pairs from paired-end sequencing. All pairs must be complete. Example of the input data format is provided in the help below."/> - <param name="sample" label="Sample size" type="integer" value="500000" min="10000"/> + + <conditional name="read_sampling"> + <param name="do_sampling" type="boolean" truevalue="true" falsevalue="false" checked="True" label="Use maximum processable sequence reads" /> + <when value="true"> + <!-- pass --> + <param name="sample" label="Sample size" hidden="True" type="integer" value="0" help="Number of sequence reads for clustering"/> + </when> + <when value="false"> + <param name="sample" label="Sample size" type="integer" value="500000" min="10000" help="Number of reads for clustering"/> + </when> + </conditional> + <conditional name="advanced_options"> <param name="advanced" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Advanced options" /> @@ -98,9 +109,10 @@ <param name="keep_names" label="Keep original read names" type="boolean" truevalue="--keep_names" falsevalue="" checked="false" help="By default, reads are renamed using integers. Use this option if you want to keep original names."/> <conditional name="options"> <param name="options" type="select" label="Similarity search options" help="Different similarity search parameters are used depending on the input data to adjust search to differences in read length and error rate"> - <option value="ILLUMINA" selected="true">Illumina reads, read length 100nt or more </option> - <option value="ILLUMINA_SHORT" selected="false">Illumina reads, shorter than 100nt (Do not use reads shorter than 50nt!) </option> + <option value="ILLUMINA" selected="true">Illumina reads, default, all-to-all search uses mgblast, minimal identity 90% </option> <option value="ILLUMINA_DUST_OFF" selected="false">Illumina reads, no masking of low complexity repeats </option> + <option value="ILLUMINA_SENSITIVE_MGBLAST" selected="false">all-to-all search is performed using mgblast (W8, min PID 80) slow, experimental feature!</option> + <option value="ILLUMINA_SENSITIVE_BLASTPLUS" selected="false">all-to-all search is performed using blastn (W6, min PID 80) very slow, experimental feature!</option> </param> </conditional> </when>