Mercurial > repos > iuc > fastk_logex
changeset 3:9b1aebbaec34 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 814017d155da225181f3b41c25f99f4c23f03835
| author | iuc |
|---|---|
| date | Sat, 10 May 2025 09:09:02 +0000 |
| parents | ec82f2b95e89 |
| children | 94217ea28453 |
| files | logex.xml |
| diffstat | 1 files changed, 242 insertions(+), 44 deletions(-) [+] |
line wrap: on
line diff
--- a/logex.xml Wed Feb 19 11:17:07 2025 +0000 +++ b/logex.xml Sat May 10 09:09:02 2025 +0000 @@ -1,4 +1,4 @@ -<tool id="fastk_logex" name="FastK Logex" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2" license="MIT"> +<tool id="fastk_logex" name="FastK Logex" version="@TOOL_VERSION@+galaxy3" profile="24.2" license="MIT"> <description>Performs binary operations on the generated Ktab files from FASTK suite</description> <macros> <import>macros.xml</import> @@ -6,47 +6,119 @@ <expand macro="xrefs"/> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ - mkdir -p logex_ktabs - && mkdir -p input_files - && cp '$input_ktab1' input_files/input1.ktab - && ln -s '$input_ktab1_tar' input1.tar - && tar -xf input1.tar - && mv ktabfiles ktabfiles_in1 - && mv "\$(find ktabfiles_in1 -type f -name '*.ktab.1')" "ktabfiles_in1/.input1.ktab.1" - && cp '$input_ktab2' input_files/input2.ktab - && ln -s '$input_ktab2_tar' input2.tar - && tar -xf input2.tar - && mv ktabfiles ktabfiles_in2 - && mv "\$(find ktabfiles_in2 -type f -name '*.ktab.1')" "ktabfiles_in2/.input2.ktab.1" - && mv ktabfiles_in1/.input1.ktab.1 input_files/ - && mv ktabfiles_in2/.input2.ktab.1 input_files/ && - #if $operation_selector == 'and': - Logex -T\${GALAXY_SLOTS:-8} -h 'out = A&.B' input_files/input1.ktab input_files/input2.ktab - #elif $operation_selector == 'or': - Logex -T\${GALAXY_SLOTS:-8} -h 'out = A|.B' input_files/input1.ktab input_files/input2.ktab - #elif $operation_selector == 'minus': - Logex -T\${GALAXY_SLOTS:-8} -h 'out = A-B' input_files/input1.ktab input_files/input2.ktab - #elif $operation_selector == 'xor': - Logex -T\${GALAXY_SLOTS:-8} -h 'out = A^B' input_files/input1.ktab input_files/input2.ktab - #elif $operation_selector == 'unionsum': - Logex -T\${GALAXY_SLOTS:-8} -h 'out = A&+B' input_files/input1.ktab input_files/input2.ktab + mkdir -p logex_ktabs && + mkdir -p input_files && + #if $input_type.input_type_selector != 'collection' + cp '$input_ktab1' input_files/input1.ktab && + ln -s '$input_ktab1_tar' input1.tar && + tar -xf input1.tar && + mv ktabfiles ktabfiles_in1 && + mv "\$(find ktabfiles_in1 -type f -name '*.ktab.1')" "ktabfiles_in1/.input1.ktab.1" && + cp '$input_ktab2' input_files/input2.ktab && + ln -s '$input_ktab2_tar' input2.tar && + tar -xf input2.tar && + mv ktabfiles ktabfiles_in2 && + mv "\$(find ktabfiles_in2 -type f -name '*.ktab.1')" "ktabfiles_in2/.input2.ktab.1" && + mv ktabfiles_in1/.input1.ktab.1 input_files/ && + mv ktabfiles_in2/.input2.ktab.1 input_files/ && + #if $input_type.operation_selector == 'and' + Logex -T\${GALAXY_SLOTS:-8} -h 'out = A&.B' input_files/input1.ktab input_files/input2.ktab && + #elif $input_type.operation_selector == 'or' + Logex -T\${GALAXY_SLOTS:-8} -h 'out = A|.B' input_files/input1.ktab input_files/input2.ktab && + #elif $input_type.operation_selector == 'minus' + Logex -T\${GALAXY_SLOTS:-8} -h 'out = A-B' input_files/input1.ktab input_files/input2.ktab && + #elif $input_type.operation_selector == 'xor' + Logex -T\${GALAXY_SLOTS:-8} -h 'out = A^B' input_files/input1.ktab input_files/input2.ktab && + #elif $input_type.operation_selector == 'unionsum' + Logex -T\${GALAXY_SLOTS:-8} -h 'out = A&+B' input_files/input1.ktab input_files/input2.ktab && + #end if + #else + #for $i, $j in enumerate($input_type.input_ktab_collection): + cp "$j" input_files/${i+1}.ktab && + #end for + #for $p, $q in enumerate($input_type.input_ktab_collection_tar): + ln -s "$q" input_files/input_ktab_${p+1}.tar && + tar -tf input_files/input_ktab_${p+1}.tar | grep '/\.[^/]*$' | tar --strip-components=1 -xf input_files/input_ktab_${p+1}.tar -C input_files/ -T - && + rm input_files/input_ktab_${p+1}.tar && + #end for + COUNT=\$(ls -1 input_files/*.ktab 2>/dev/null | wc -l) && + if [ "\$COUNT" -ge 2 ]; then + #if $input_type.operation_sel.operation_selector_collection == 'unionsum': + EXPRESSION="out=\$(seq -s '&+' 0 \$((COUNT-1)) | tr '0-9' 'A-Z')" && + #elif $input_type.operation_sel.operation_selector_collection == 'and': + EXPRESSION="out=\$(seq -s '&.' 0 \$((COUNT-1)) | tr '0-9' 'A-Z')" && + #elif $input_type.operation_sel.operation_selector_collection == 'minus': + EXPRESSION="out=\$(seq -s '-' 0 \$((COUNT-1)) | tr '0-9' 'A-Z')" && + #elif $input_type.operation_sel.operation_selector_collection == 'or': + EXPRESSION="out=\$(seq -s '|.' 0 \$((COUNT-1)) | tr '0-9' 'A-Z')" && + #elif $input_type.operation_sel.operation_selector_collection == 'xor': + EXPRESSION="out=\$(seq -s '^' 0 \$((COUNT-1)) | tr '0-9' 'A-Z')" && + #elif $input_type.operation_sel.operation_selector_collection == 'custom': + EXPRESSION="out=$input_type.operation_sel.custom_expression" && + #end if + Logex -T\${GALAXY_SLOTS:-8} -h "\$EXPRESSION" input_files/*.ktab; + else + echo "ERROR: Logex needs atleast 2 Ktab files" >&2 && exit 1; + fi && #end if - && cp *.ktab logex_ktabs/ - && cp .*.ktab* logex_ktabs/ - && tar -cf logex_ktab.tar input_files/ logex_ktabs/ + cp *.ktab logex_ktabs/ && + cp .*.ktab* logex_ktabs/ && + tar -cf logex_ktab.tar input_files/ logex_ktabs/ ]]></command> <inputs> - <param name="input_ktab1" type="data" format="fastk_ktab" label="Input FastK ktab file (first)"/> - <param name="input_ktab1_tar" type="data" format="fastk_ktab_tar" label="Associated FastK TAR file consisting of intermediate .ktab files"/> - <param name="input_ktab2" type="data" format="fastk_ktab" label="Input FastK ktab file (second)"/> - <param name="input_ktab2_tar" type="data" format="fastk_ktab_tar" label="Associated FastK TAR file consisting of intermediate .ktab files"/> - <param name="operation_selector" type="select" label="Select Operation to Perform" help="Select the operation to be performed on the input ktab files."> - <option value="and">AND</option> - <option value="or">OR</option> - <option value="minus">Minus</option> - <option value="unionsum">Unionsum</option> - <option value="xor">XOR</option> - </param> + <conditional name="input_type"> + <param name="input_type_selector" type="select" label="Single Ktab file or Ktab Collection"> + <option value="single">Single Ktab file</option> + <option value="collection">Ktab files Collection</option> + </param> + <when value="single"> + <param name="input_ktab1" type="data" format="fastk_ktab" label="Input FastK ktab file (first)"/> + <param name="input_ktab1_tar" type="data" format="fastk_ktab_tar" label="Associated FastK TAR file consisting of intermediate .ktab files"/> + <param name="input_ktab2" type="data" format="fastk_ktab" label="Input FastK ktab file (second)"/> + <param name="input_ktab2_tar" type="data" format="fastk_ktab_tar" label="Associated FastK TAR file consisting of intermediate .ktab files"/> + <param name="operation_selector" type="select" label="Select Operation to Perform" help="Select the operation to be performed on the input ktab files."> + <option value="and">AND</option> + <option value="or">OR</option> + <option value="minus">Minus</option> + <option value="unionsum">Unionsum</option> + <option value="xor">XOR</option> + </param> + </when> + <when value="collection"> + <param name="input_ktab_collection" type="data_collection" collection_type="list" format="fastk_ktab" label="Input FastK ktab Collection"/> + <param name="input_ktab_collection_tar" type="data_collection" format="fastk_ktab_tar" label="Associated FastK TAR file consisting of intermediate .ktab files"/> + <conditional name="operation_sel"> + <param name="operation_selector_collection" type="select" label="Select Operation to Perform" help="Select the operation to be performed on the input ktab files."> + <option value="and">AND</option> + <option value="or">OR</option> + <option value="minus">Minus</option> + <option value="unionsum">Unionsum</option> + <option value="xor">XOR</option> + <option value="custom">Custom Logical Expression</option> + </param> + <when value="and"/> + <when value="or"/> + <when value="minus"/> + <when value="unionsum"/> + <when value="xor"/> + <when value="custom"> + <param name="custom_expression" type="text" label="Custom Logical Expression" value="out=" help="Enter a custom logical expression based on number of your input ktab files. For Eg: For 3 Ktab files the expression can be out=(A^B)-C"> + <sanitizer invalid_char=""> + <valid> + <add value="+"/> + <add value="-"/> + <add value="|"/> + <add value="."/> + <add value="^"/> + <add value="="/> + <add value="&"/> + </valid> + </sanitizer> + </param> + </when> + </conditional> + </when> + </conditional> </inputs> <outputs> <data name="fastk_hist_out" format="fastk_hist" from_work_dir="out.hist" label="${tool.name} on ${on_string}: Logex .hist file"/> @@ -55,11 +127,14 @@ </outputs> <tests> <test expect_num_outputs="3"> - <param name="input_ktab1" value="fastq1.ktab"/> - <param name="input_ktab1_tar" value="fastk_in1.tar"/> - <param name="input_ktab2" value="fastq2.ktab"/> - <param name="input_ktab2_tar" value="fastk_in2.tar"/> - <param name="operation_selector" value="AND"/> + <conditional name="input_type"> + <param name="input_type_selector" value="single"/> + <param name="input_ktab1" value="fastq1.ktab"/> + <param name="input_ktab1_tar" value="fastk_in1.tar"/> + <param name="input_ktab2" value="fastq2.ktab"/> + <param name="input_ktab2_tar" value="fastk_in2.tar"/> + <param name="operation_selector" value="and"/> + </conditional> <output name="fastk_hist_out" ftype="fastk_hist"> <assert_contents> <has_size value="262164"/> @@ -81,12 +156,135 @@ </assert_contents> </output> </test> + <test expect_num_outputs="3"> + <conditional name="input_type"> + <param name="input_type_selector" value="collection"/> + <param name="input_ktab_collection"> + <collection type="list"> + <element name="input1" value="fastq1.ktab"/> + <element name="input2" value="fastq2.ktab"/> + </collection> + </param> + <param name="input_ktab_collection_tar"> + <collection type="list"> + <element name="input1" value="fastk_in1.tar"/> + <element name="input2" value="fastk_in2.tar"/> + </collection> + </param> + <conditional name="operation_sel"> + <param name="operation_selector_collection" value="and"/> + </conditional> + </conditional> + <output name="fastk_hist_out" ftype="fastk_hist"> + <assert_contents> + <has_size value="262164"/> + </assert_contents> + </output> + <output name="fastk_ktab_out" ftype="fastk_ktab"> + <assert_contents> + <has_size value="2064"/> + </assert_contents> + </output> + <output name="fastk_ktab_files" ftype="fastk_ktab_tar"> + <assert_contents> + <has_archive_member path="logex_ktabs/out.ktab"/> + <has_archive_member path="logex_ktabs/.out.ktab.1"/> + <has_archive_member path="input_files/1.ktab"/> + <has_archive_member path="input_files/.1.ktab.1"/> + <has_archive_member path="input_files/2.ktab"/> + <has_archive_member path="input_files/.2.ktab.1"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="3"> + <conditional name="input_type"> + <param name="input_type_selector" value="collection"/> + <param name="input_ktab_collection"> + <collection type="list"> + <element name="input1" value="fastq1.ktab"/> + <element name="input2" value="fastq2.ktab"/> + </collection> + </param> + <param name="input_ktab_collection_tar"> + <collection type="list"> + <element name="input1" value="fastk_in1.tar"/> + <element name="input2" value="fastk_in2.tar"/> + </collection> + </param> + <conditional name="operation_sel"> + <param name="operation_selector_collection" value="unionsum"/> + </conditional> + </conditional> + <output name="fastk_hist_out" ftype="fastk_hist"> + <assert_contents> + <has_size value="262164"/> + </assert_contents> + </output> + <output name="fastk_ktab_out" ftype="fastk_ktab"> + <assert_contents> + <has_size value="2064"/> + </assert_contents> + </output> + <output name="fastk_ktab_files" ftype="fastk_ktab_tar"> + <assert_contents> + <has_archive_member path="logex_ktabs/out.ktab"/> + <has_archive_member path="logex_ktabs/.out.ktab.1"/> + <has_archive_member path="input_files/1.ktab"/> + <has_archive_member path="input_files/.1.ktab.1"/> + <has_archive_member path="input_files/2.ktab"/> + <has_archive_member path="input_files/.2.ktab.1"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="3"> + <conditional name="input_type"> + <param name="input_type_selector" value="collection"/> + <param name="input_ktab_collection"> + <collection type="list"> + <element name="input1" value="fastq1.ktab"/> + <element name="input2" value="fastq2.ktab"/> + </collection> + </param> + <param name="input_ktab_collection_tar"> + <collection type="list"> + <element name="input1" value="fastk_in1.tar"/> + <element name="input2" value="fastk_in2.tar"/> + </collection> + </param> + <conditional name="operation_sel"> + <param name="operation_selector_collection" value="custom"/> + <param name="custom_expression" value="A&.B"/> + </conditional> + </conditional> + <output name="fastk_hist_out" ftype="fastk_hist"> + <assert_contents> + <has_size value="262164"/> + </assert_contents> + </output> + <output name="fastk_ktab_out" ftype="fastk_ktab"> + <assert_contents> + <has_size value="2064"/> + </assert_contents> + </output> + <output name="fastk_ktab_files" ftype="fastk_ktab_tar"> + <assert_contents> + <has_archive_member path="logex_ktabs/out.ktab"/> + <has_archive_member path="logex_ktabs/.out.ktab.1"/> + <has_archive_member path="input_files/1.ktab"/> + <has_archive_member path="input_files/.1.ktab.1"/> + <has_archive_member path="input_files/2.ktab"/> + <has_archive_member path="input_files/.2.ktab.1"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[ Logex tool can perform operations such as AND, OR, XOR, Minus and Unionsum on the input given input Ktab files. The tool requires two input Ktab files and their associated files (Generated in the tarball of FASTK tool with .1 extension) as inputs to perform various binary operations. + + The tool also supports Ktab file collections as input. The user can select the operation to be performed on the input Ktab files. ]]></help> <expand macro="citations"/>