Mercurial > repos > earlhaminst > t_coffee
changeset 7:0a189243186d draft
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 88e1592fa528db1941bce52c588d4347a69cc745
| author | earlhaminst |
|---|---|
| date | Wed, 18 Sep 2019 06:37:40 -0400 |
| parents | c67bd5acbae2 |
| children | ae69d14b6fbf |
| files | filter_by_fasta_ids.py t_coffee.xml |
| diffstat | 2 files changed, 38 insertions(+), 44 deletions(-) [+] |
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--- a/filter_by_fasta_ids.py Wed Apr 25 11:15:13 2018 -0400 +++ b/filter_by_fasta_ids.py Wed Sep 18 06:37:40 2019 -0400 @@ -35,15 +35,11 @@ def main(): - ''' the main function''' - used_sequences = set() work_summary = {'wanted': 0, 'found': 0, 'duplicates': 0} - targets = [] with open(sys.argv[1]) as f_target: - for line in f_target.readlines(): - targets.append(">%s" % line.strip().upper()) + targets = [">%s" % _.strip().upper() for _ in f_target] work_summary['wanted'] = len(targets)
--- a/t_coffee.xml Wed Apr 25 11:15:13 2018 -0400 +++ b/t_coffee.xml Wed Sep 18 06:37:40 2019 -0400 @@ -7,47 +7,45 @@ <exit_code range="1:" level="fatal" /> </stdio> <version_command> - t_coffee -version | grep Version +t_coffee -version | grep Version </version_command> - <command use_shared_home="false"> -<![CDATA[ - #if str($input_type.filter_fasta) == 'yes' - #set $input = 'temp.fasta' - python '$__tool_directory__/filter_by_fasta_ids.py' '$input_type.identifiers' '$input_type.fasta_input' > temp.fasta && - #end if + <command use_shared_home="false"><![CDATA[ +#if str($input_type.filter_fasta) == 'yes' + #set $input = 'temp.fasta' + python '$__tool_directory__/filter_by_fasta_ids.py' '$input_type.identifiers' '$input_type.fasta_input' > temp.fasta && +#end if - #set $method_opt = '' - #if $method01 - #set $method_opt += str($method01) + ',' - #end if - #if $method02 - #set $method_opt += str($method02) + ',' - #end if - #if $method03 - #set $method_opt += str($method03) + ',' +#set $method_opt = '' +#if $method01 + #set $method_opt += str($method01) + ',' +#end if +#if $method02 + #set $method_opt += str($method02) + ',' +#end if +#if $method03 + #set $method_opt += str($method03) + ',' +#end if +#if $method_opt + #set $method_opt = '-method ' + $method_opt[:-1] +#end if + +#set $output_opt = '' +#if $outputs + #set $outputs_arr = str($outputs).split(',') + #for $o in $outputs_arr + #if $o != 'dnd' + #set $output_opt += $o + ',' #end if - #if $method_opt - #set $method_opt = '-method ' + $method_opt[:-1] - #end if + #end for +#else + #set $outputs_arr = [] +#end if +#if $output_opt + #set $output_opt = '-output ' + $output_opt[:-1] +#end if - #set $output_opt = '' - #if $outputs - #set $outputs_arr = str($outputs).split(',') - #for $o in $outputs_arr - #if $o != 'dnd' - #set $output_opt += $o + ',' - #end if - #end for - #else - #set $outputs_arr = [] - #end if - #if $output_opt - #set $output_opt = '-output ' + $output_opt[:-1] - #end if - - t_coffee '$input' $method_opt $output_opt -n_core \${GALAXY_SLOTS:-1} -run_name t_coffee_out -quiet -]]> - </command> +t_coffee '$input' $method_opt $output_opt -n_core \${GALAXY_SLOTS:-1} -run_name t_coffee_out -quiet + ]]></command> <inputs> <conditional name="input_type"> <param name="filter_fasta" type="select" label="Filter FASTA input?"> @@ -147,7 +145,7 @@ <output name="fasta_aln" file="output2.fasta" ftype="fasta" /> </test> </tests> - <help> + <help><![CDATA[ **What it does** This tool is a wrapper for the T-Coffee multiple sequence alignment suite. The input is a set of sequences in FASTA format. Apart from running on the complete FASTA input, it can also run on a subset of sequences by providing a list of the FASTA IDs. @@ -192,7 +190,7 @@ >1ihvA NF-RVYYRDSRDPVWKGPA-KLLWKGEGAV-------VIQDN-------S DI--------------KVVPRRKAK-----IIRD - </help> + ]]></help> <citations> <citation type="doi">10.1006/jmbi.2000.4042</citation> </citations>