Mercurial > repos > iuc > merqury
diff merqury.xml @ 2:589078edd230 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury commit 726df1fe4e8d703f62e1b9062bab1627c94ce746"
| author | iuc |
|---|---|
| date | Mon, 25 Apr 2022 11:20:41 +0000 |
| parents | 39edec572bae |
| children | f8113c25bc6b |
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--- a/merqury.xml Thu Nov 11 16:38:42 2021 +0000 +++ b/merqury.xml Mon Apr 25 11:20:41 2022 +0000 @@ -17,7 +17,10 @@ #else && ln -s '$mode.assembly_options.assembly_01' assembly.fasta #end if - && merqury.sh read-db.meryl assembly.fasta ${label} + && merqury.sh read-db.meryl assembly.fasta ${label} + #if 'log' in $output_selector + &> $log_file + #end if && mv ${label}* output_files && find . -maxdepth 1 -name 'assembly_only*' -type f -print0 | xargs -0r mv -t output_files #else @@ -32,6 +35,9 @@ && ln -s '$mode.assembly_options.assembly_02' assembly_02.fasta #end if && merqury.sh read-db.meryl assembly_01.fasta assembly_02.fasta ${label} + #if 'log' in $output_selector + &> $log_file + #end if && mv ${label}* output_files && find . -maxdepth 1 -name 'assembly_only*' -type f -print0 | xargs -0r mv -t output_files #end if @@ -47,6 +53,9 @@ && ln -s '$mode.assembly_options.assembly_01' assembly.fasta #end if && merqury.sh read-db.meryl pat.meryl mat.meryl assembly.fasta ${label} + #if 'log' in $output_selector + &> $log_file + #end if && mv ${label}* output_files && find . -maxdepth 1 -name 'assembly_only*' -type f -print0 | xargs -0r mv -t output_files #else @@ -61,10 +70,14 @@ && ln -s '$mode.assembly_options.assembly_02' assembly_02.fasta #end if && merqury.sh read-db.meryl pat.meryl mat.meryl assembly_01.fasta assembly_02.fasta ${label} + #if 'log' in $output_selector + &> $log_file + #end if && mv ${label}* output_files && find . -maxdepth 1 -name 'assembly_only*' -type f -print0 | xargs -0r mv -t output_files #end if #end if + ]]> </command> <inputs> <conditional name="mode"> @@ -144,6 +157,7 @@ <option value="stats" selected="true">Stats file</option> <option value="bed">BED: hap-mer tracks</option> <option value="wig">WIG: hap-mer tracks</option> + <option value="log">Log file</option> </param> </inputs> <outputs> @@ -171,6 +185,9 @@ <discover_datasets pattern="(?P<name>.+)\.stats" format="tabular" directory="output_files"/> <filter>"stats" in output_selector</filter> </collection> + <data name="log_file" format="txt" label="${tool.name} on ${on_string}: log file"> + <filter>"log" in output_selector</filter> + </data> </outputs> <tests> <!--Test 01: trio mode--> @@ -300,6 +317,26 @@ <element name="output_04" file="output_04_qv.tabular" ftype="tabular"/> </output_collection> </test> + <!--Test 05: log file--> + <test expect_num_outputs="2"> + <conditional name="mode"> + <param name="options" value="trio"/> + <param name="meryldb_F1" value="child.meryldb" ftype="meryldb"/> + <param name="meryldb_PAT" value="pat.meryldb" ftype="meryldb"/> + <param name="meryldb_MAT" value="mat.meryldb" ftype="meryldb"/> + <conditional name="assembly_options"> + <param name="number_assemblies" value="two"/> + <param name="assembly_01" value="assembly.fasta.gz" ftype="fasta.gz"/> + <param name="assembly_02" value="assembly_02.fasta.gz" ftype="fasta.gz"/> + </conditional> + </conditional> + <param name="label" value="output_05"/> + <param name="output_selector" value="qv,log"/> + <output_collection name="qv_files" type="list" count="1"> + <element name="output_05" file="output_04_qv.tabular" ftype="tabular"/> + </output_collection> + <output name="log_file" file="output_05_log.txt" ftype="txt" lines_diff='4'/> + </test> </tests> <help><![CDATA[ .. class:: infomark