| Next changeset 1:9625ddf6eed5 (2018-03-06) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot commit 2cbbe72925991a2db566d6e2bb3a61e8e7131f3e |
|
added:
msaboot.xml test-data/log.txt test-data/msa.fasta test-data/out.phylip |
| b |
| diff -r 000000000000 -r 48b414c7d38e msaboot.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/msaboot.xml Mon Feb 19 14:07:33 2018 -0500 |
| [ |
| @@ -0,0 +1,86 @@ +<?xml version="1.0"?> +<tool id="msaboot" name="MSABOOT" version="@VERSION@"> + <description>Output PHYLIP file with bootstrapped multiple sequence alignment data</description> + <macros> + <token name="@VERSION@">0.1.0</token> + </macros> + <requirements> + <requirement type="package" version="@VERSION@">msaboot</requirement> + </requirements> + <version_command>msaboot --version</version_command> + <command detect_errors="aggressive"> + <![CDATA[ +msaboot -i '$input' -n $number -o '$output' +#if $save_logfile: + > '$log' 2>&1 +#end if + ]]> + </command> + <inputs> + <param name="input" format="fasta" type="data" label="FASTA input file" /> + <param name="number" type="integer" value="1" min="1" label="Specify the number of bootstrapping replicates to generate." /> + <param name="save_logfile" type="boolean" truevalue="" falsevalue="" label="Output log file" /> + </inputs> + <outputs> + <data name="output" format="phylip" label="${tool.name} on ${on_string}:out.phylip" /> + <data name="log" format="txt" label="${tool.name} on ${on_string}:log_msabootpl_run.txt"> + <filter>save_logfile</filter> + </data> + </outputs> + <tests> + <test> + <param name="input" value="msa.fasta" /> + <param name="number" value="10" /> + <param name="save_logfile" value="true" /> + <output name="log" file="log.txt" ftype="txt" compare="contains" /> + <output name="output" file="out.phylip" ftype="phylip" compare="contains" /> + </test> + </tests> + <help> +<![CDATA[ + +=========== +Description +=========== + +.. class:: infomark + +A tool for creating bootstrapping replicates from Multiple Sequence Alignment data. + +.. _msaboot: https://github.com/phac-nml/msaboot + +----- + +----- +Input +----- +Input file location of FASTA file containing Multiple Sequence Alignment data(-i) + +---------- +Parameters +---------- +Number of bootstrapping replicates (-n) + +------ +Output +------ + +This tool produces two output files, one of which is optional (the log file). + +(A) The bootstrapped replicates in Phylip format. + +(B) The optional log file, containing information about the msaboot run to bootstrap the multiple sequence alignment data. + +]]> + </help> + <citations> + <citation type="bibtex"> + @misc{GitHubmsaboot, + title = {msaboot}, + publisher = {phac-nml}, + journal = {GitHub repository}, + url = {https://github.com/phac-nml/msaboot}, + } + </citation> + </citations> +</tool> |
| b |
| diff -r 000000000000 -r 48b414c7d38e test-data/log.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/log.txt Mon Feb 19 14:07:33 2018 -0500 |
| b |
| @@ -0,0 +1,1 @@ +msaboot v0.1.0 |
| b |
| diff -r 000000000000 -r 48b414c7d38e test-data/msa.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/msa.fasta Mon Feb 19 14:07:33 2018 -0500 |
| b |
| @@ -0,0 +1,17 @@ +>1 +AAA +>2 +CCC +>3 +GGG +>4 +TTT +>5 +ACG +>6 +CGT +>7 +GTA +>8 +TAC + |
| b |
| diff -r 000000000000 -r 48b414c7d38e test-data/out.phylip --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.phylip Mon Feb 19 14:07:33 2018 -0500 |
| b |
| @@ -0,0 +1,1 @@ + |