Mercurial > repos > padge > trimal
diff trimal.xml @ 0:b15a3147e604 draft
"planemo upload for repository https://github.com/inab/trimal commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
| author | padge |
|---|---|
| date | Fri, 25 Mar 2022 17:10:43 +0000 |
| parents | |
| children | 0d53577b962f |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/trimal.xml Fri Mar 25 17:10:43 2022 +0000 @@ -0,0 +1,123 @@ +<tool id="trimal" name="trimAl: a tool for automated alignment trimming" version="0.1.0" python_template_version="3.5"> + <requirements> + <requirement type="package" version="1.4.1">trimal</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + trimal -in $input1 -out $trimmed_output -htmlout $html_summary ${out_format_selector} + #if $trimming_mode.mode_selector == "custom" + -gapthreshold $trimming_mode.gapthreshold + -simthreshold $trimming_mode.simthreshold + -cons $trimming_mode.cons + #else: + $trimming_mode.mode_selector + #end if + ; + + ]]></command> + <inputs> + <param name="input1" type="data" format="fasta,clustal,pir,phylip,nexus" multiple="false" label="Alignment file (clustal, fasta, NBRF/PIR, nexus, phylip3.2, phylip)" optional="false" /> + <conditional name="trimming_mode"> + <param name="mode_selector" type="select" label="Select trimming mode from the list"> + <option value="-nogaps">nogaps. Remove all positions with gaps in the alignment.</option> + <option value="-noallgaps">noallgaps. Remove columns composed only by gaps.</option> + <option value="-gappyout">gappyout. Only uses information based on gaps' distribution. (see User Guide)</option> + <option value="-strict">strict. (see User Guide)</option> + <option value="-strictplus">strictplus. (see User Guide)</option> + <option value="custom">Custom mode</option> + </param> + <when value="custom"> + <param argument="-gapthreshold" type="float" optional="true" value="0.9" min="0.0" max="1.0" label="gap threshold" help="1 - (fraction of sequences with a gap allowed). Range: [0 - 1]" multiple="false"/> + <param argument="-simthreshold" type="float" optional="true" value="0.9" min="0.0" max="1.0" label="similarity threshold" help="Minimum average similarity allowed. Range: [0 - 1]" multiple="false"/> + <param argument="-cons" type="integer" optional="true" value="50" min="0" max="100" label="min conservance percentage" help="Minimum percentage of the positions in the original alignment to conserve." multiple="false"/> + + </when> + </conditional> + <param name="out_format_selector" type="select" label="Select trimmed alignment output format from the list"> + <option value="-clustal">CLUSTAL format</option> + <option value="-fasta">FASTA format</option> + <option value="-fasta_m10">FASTA format. Sequences name length up to 10 characters.</option> + <option value="-nbrf">NBRF/PIR format</option> + <option value="-nexus">NEXUS format</option> + <option value="-mega">MEGA format</option> + <option value="-phylip">PHYLIP/PHYLIP4 format</option> + <option value="-phylip_m10">PHYLIP/PHYLIP4 format. Sequences name length up to 10 characters</option> + <option value="-phylip_paml">PHYLIP format compatible with PAML</option> + <option value="-phylip_paml_m10">PHYLIP format compatible with PAML. Sequences name length up to 10 characters.</option> + <option value="-phylip3.2">PHYLIP3.2 format</option> + <option value="-phylip3.2_m10">PHYLIP3.2 format. Sequences name length up to 10 characters.</option> + </param> + </inputs> + <outputs> + <data name="trimmed_output" format="fasta" label="Trimmed alignment."/> + <data name="html_summary" format="html" label="trimal html summary."/> + </outputs> + <tests> + <test> + <param name="input1" value="example.009.AA.fasta"/> + <param name="mode_selector" value="-gappyout" /> + <param name="out_format_selector" value="-mega" /> + <output name="trimmed_output" file="trimmed_example.009.AA.mega" lines_diff="2"/> + <output name="html_summary" file="trimmed_example.009.AA.html"/> + </test> + <test> + <param name="input1" value="example.009.AA.fasta"/> + <param name="mode_selector" value="custom" /> + <param name="gapthreshold" value="0.5" /> + <param name="simthreshold" value="0.5" /> + <param name="cons" value="5" /> + <param name="out_format_selector" value="-phylip_paml_m10" /> + <output name="trimmed_output" file="custom_trimmed_example.009.AA.phy" /> + <output name="html_summary" file="custom_trimmed_example.009.AA.html"/> + </test> + </tests> + <help><![CDATA[ +Modes + -nogaps Remove all positions with gaps in the alignment. + -noallgaps Remove columns composed only by gaps. + -gappyout Use automatic selection on "gappyout" mode. This method only uses information based on gaps' distribution. (see User Guide). + -strict Use automatic selection on "strict" mode. (see User Guide). + -strictplus Use automatic selection on "strictplus" mode. (see User Guide). + trimAl v1.4.rev15 build[2013-12-17]. 2009-2013. Salvador Capella-Gutierrez and Toni Gabaldón. + +Custom mode parameters + -gt -gapthreshold <n> 1 - (fraction of sequences with a gap allowed). + -st -simthreshold <n> Minimum average similarity allowed. + -cons <n> Minimum percentage of the positions in the original alignment to conserve. + +Output formats + -nbrf Output file in NBRF/PIR format + -mega Output file in MEGA format + -nexus Output file in NEXUS format + -clustal Output file in CLUSTAL format + -fasta Output file in FASTA format + -fasta_m10 Output file in FASTA format. Sequences name length up to 10 characters. + -phylip Output file in PHYLIP/PHYLIP4 format + -phylip_m10 Output file in PHYLIP/PHYLIP4 format. Sequences name length up to 10 characters. + -phylip_paml Output file in PHYLIP format compatible with PAML + -phylip_paml_m10 Output file in PHYLIP format compatible with PAML. Sequences name length up to 10 characters. + -phylip3.2 Output file in PHYLIP3.2 format + -phylip3.2_m10 Output file in PHYLIP3.2 format. Sequences name length up to 10 characters. + +trimAl webpage: http://trimal.cgenomics.org + +This program is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, the last available version. + +Please cite: + trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. + Salvador Capella-Gutierrez; Jose M. Silla-Martinez; Toni Gabaldon. + Bioinformatics 2009, 25:1972-1973. + ]]></help> + <citations> + <citation type="bibtex"> +@misc{githubTrimAl, + author = {LastTODO, FirstTODO}, + year = {TODO}, + title = {TrimAl}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/inab/trimal}, +}</citation> + </citations> +</tool> \ No newline at end of file