Mercurial > repos > iuc > recentrifuge
diff recentrifuge.xml @ 1:fe733f05c2f8 draft
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit 9142693589056424fb64869b69dbc08b179f57ee
| author | iuc |
|---|---|
| date | Fri, 26 Aug 2022 10:57:30 +0000 |
| parents | 09b7b0b2e2c2 |
| children | b5407cc2bf51 |
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--- a/recentrifuge.xml Mon Jun 27 11:03:22 2022 +0000 +++ b/recentrifuge.xml Fri Aug 26 10:57:30 2022 +0000 @@ -7,10 +7,28 @@ <macros> <import>macro.xml</import> </macros> + <expand macro='edam'/> <expand macro='xrefs'/> <expand macro="requirements" /> <expand macro="version_command" /> <command detect_errors="aggressive"><![CDATA[ + #import re + #*====================================== + Make a dir with all input files + ======================================*# + mkdir input_dir && + #for $input in $input_file + #set input_identifier = re.sub('[^\s\w\-]', '_', str($input.element_identifier)) + #if $file_type.filetype == "centrifuge" + ln -s '$input' 'input_dir/${input_identifier}.out' && + #else if $file_type.filetype == "clark" + ln -s '$input' 'input_dir/${input_identifier}.csv' && + #else if $file_type.filetype == "kraken" + ln -s '$input' 'input_dir/${input_identifier}.krk' && + #else + ln -s '$input' 'input_dir/$input_identifier' && + #end if + #end for #*====================================== database input ======================================*# @@ -19,23 +37,25 @@ #*====================================== Recentrifuge input file ======================================*# + #if $file_type.filetype == "centrifuge" - -f '$input_file' + -f input_dir + #set $default_scoring = 'SHEL' + #else if $file_type.filetype == "kraken" + -k input_dir + #set $default_scoring = 'KRAKEN' + #else if $file_type.filetype == "clark" + -r input_dir #set $default_scoring = 'SHEL' #else if $file_type.filetype == "lmat" - -l '$input_file' + -l input_dir #set $default_scoring = 'LMAT' - #else if $file_type.filetype == "clark" - -r '$input_file' - #set $default_scoring = 'SHEL' - #else if $file_type.filetype == "kraken" - -k '$input_file' - #set $default_scoring = 'KRAKEN' #else if $file_type.filetype == "generic" - -g '$input_file' + -g input_dir --format '$file_type.format' #set $default_scoring = 'GENERIC' #end if + #*====================================== Output options ======================================*# @@ -83,12 +103,12 @@ #*====================================== Log file output ======================================*# - &> $logfile + | tee "$logfile" ]]> </command> <inputs> <!-- INPUT FILES --> - <param name="input_file" type="data" format="tabular" label="Select taxonomy file tabular formated"/> + <param name="input_file" type="data" format="tabular" multiple="true" optional="false" label="Select taxonomy file tabular formated"/> <conditional name="file_type"> <param name="filetype" type="select" display="radio" label="Type of input file (Centrifuge, CLARK, Generic, Kraken, LMAT)" help="(-f, -r, -g, -k, -l)"> <option value="centrifuge">Centrifuge</option> @@ -126,6 +146,7 @@ <option value="TSV" >TSV</option> </param> <param argument="--nohtml" type="boolean" truevalue="--nohtml" falsevalue="" label="Suppress saving the HTML output file" help="remove html output"/> + <param name="no_logfile" type="boolean" truevalue="True" falsevalue="False" label="Remove the log file"/> </section> <!-- ADVANCED OPTIONS --> <section name="advanced_option" title="Coarse tuning of algorithm parameters"> @@ -184,7 +205,9 @@ <data name="html_report" format="html" from_work_dir="output.rcf.html" label="${tool.name} on ${on_string}: html report"> <filter> output_option['nohtml'] == False</filter> </data> - <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log file"/> + <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log file"> + <filter> output_option['no_logfile'] == False </filter> + </data> <data name="data_csv" format="tabular" from_work_dir="output.rcf.data.csv" label="${tool.name} on ${on_string}: data.csv"> <filter> output_option['extra'] == 'CSV' </filter> </data> @@ -270,6 +293,29 @@ <output name="stat_tsv" file="kraken_test/test3_rcf.stat.tsv" lines_diff="2"/> <output name="logfile" file="kraken_test/test3_tsv.log" lines_diff="12"/> </test> + <test expect_num_outputs="3"> <!-- Test sumarized output TEST_4 --> + <section name="database"> + <param name="database_name" value="test-db-2022"/> + </section> + <param name="input_file" value="centrifuge_test/centrifuge.out,centrifuge_test/centrifuge_1.out,centrifuge_test/centrifuge_2.out"/> + <conditional name="file_type"> + <param name="filetype" value="centrifuge"/> + </conditional> + <section name="output_option" > + <param name="extra" value="TSV"/> + <param name="no_logfile" value="True"/> + </section> + <section name="advanced_option"> + <param name="scoring" value="LENGTH"/> + </section> + <section name="more_advanced_option"> + <param name="summary" value="ADD"/> + <param name="strain" value="true"/> + </section> + <output name="data_tsv" file="centrifuge_test/test4_rcf.data.tsv" lines_diff="2"/> + <output name="stat_tsv" file="centrifuge_test/test4_rcf.stat.tsv" lines_diff="2"/> + <output name="html_report" file="centrifuge_test/test4_tsv.html" lines_diff="12"/> + </test> </tests> <help><![CDATA[ **What it does**