| Previous changeset 1:a3a92e30a727 (2022-07-12) Next changeset 3:39495e107274 (2022-09-28) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs commit 73f497e595363dea7f041a4374c3a9518e7b9862 |
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modified:
yahs.xml |
| b |
| diff -r a3a92e30a727 -r fc925f53cae7 yahs.xml --- a/yahs.xml Tue Jul 12 06:39:08 2022 +0000 +++ b/yahs.xml Wed Jul 27 09:26:18 2022 +0000 |
| [ |
| @@ -2,7 +2,7 @@ <description>yet another HI-C scaffolding tool</description> <macros> <token name="@VERSION@">1.2a</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> </macros> <requirements> <requirement type="package" version="@VERSION@">yahs</requirement> @@ -53,8 +53,11 @@ #end if $function.no_contig_ec $function.no_scaffold_ec - -o yahs_out && - ls -lah && + -o yahs_out + #if $log_out + 2> output.log + #end if + && ls -lah && python '$__tool_directory__/move_files.py' && ls -lah ./* #else: @@ -65,6 +68,9 @@ -l $function.length #end if -o output.fasta + #if $log_out: + 2> output.log + #end if #end if ]]></command> <inputs> @@ -85,11 +91,11 @@ The enzyme frequency in contigs is used to normalize the Hi-C interaction frequency. Note that you need to specify the actual sequence of the cutting site for a restriction enzyme and not the enzyme name. You can also specify DNASE as an enzyme if you use an enzyme-free prep, e.g. Omin-C."> - <option value="not_especified">Not especified</option> + <option value="not_specified">Not specified</option> <option value="preconfigured">Preconfigured restriction enzymes</option> <option value="specific">Enter a specific sequence</option> </param> - <when value="not_especified"/> + <when value="not_specified"/> <when value="preconfigured"> <param name="preconfigured_enzymes" argument="-e" type="select" label="Preconfigured enzymes"> <option value="dovetail">Dovetail Chicago, Dovetail Hi-C or Phase: GATC</option> @@ -115,6 +121,7 @@ <param name="length" type='integer' label="Output fasta line length" value="60" min="1"/> </when> </conditional> + <param name="log_out" type="boolean" label="Output log file?" truevalue="yes" falsevalue="no"/> </inputs> <outputs> <!-- INITIAL ROUNDS --> @@ -140,6 +147,9 @@ <data format="fasta" name="fasta_from_agp" label="${tool.name} on ${on_string}: agp to fasta" from_work_dir="output.fasta"> <filter>function['function_select'] == "agp_to_fasta"</filter> </data> + <data format="txt" name="log_file" from_work_dir="output.log" label="${tool.name} ${on_string}, log file"> + <filter>log_out</filter> + </data> </outputs> <tests> <test expect_num_outputs="5"> @@ -215,7 +225,25 @@ <param name="length" value="20"/> </conditional> <output name="fasta_from_agp" file="test_05.fasta" ftype="fasta"/> - <!-- COMMAND: agp_to_fasta teast.fasta test.agp -l 20 -o test_4 --> + <!-- COMMAND: agp_to_fasta test.fasta test.agp -l 20 -o test_4 --> + </test> + <test expect_num_outputs="6"> + <conditional name="function"> + <param name="function_select" value="yahs"/> + <param name="fasta" value="test.fasta"/> + <param name="bfile" value="test.bed"/> + <param name="agp" value="test.agp"/> + <param name="res" value="50000,100000,150000,2000000,1000000"/> + </conditional> + <param name="log_out" value="yes"/> + <output name="final_agp_out" file="test_01_scaffolds_final.agp" ftype="agp"/> + <output name="final_fasta_out" file="test_01_scaffolds_final.fa" ftype="fasta"/> + <output name="log_file" ftype="txt"> + <assert_contents> + <has_text text="[I::main] CMD: yahs"/> + </assert_contents> + </output> + <!-- COMMAND: yahs test.fasta test.bed -r 50000,100000,150000,2000000,1000000 -a test.agp -o test_1 --> </test> </tests> <help><![CDATA[ |