Mercurial > repos > iuc > ucsc_mafcoverage
diff mafCoverage.xml @ 0:2b1884fdb849 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools commit fe43201294560762b7aab73785df2f1f7828cb9e
| author | iuc |
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| date | Thu, 14 Aug 2025 11:59:27 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mafCoverage.xml Thu Aug 14 11:59:27 2025 +0000 @@ -0,0 +1,131 @@ +<tool id="ucsc_mafcoverage" name="mafCoverage" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT"> + <description>Analyse coverage by MAF files</description> + <macros> + <token name="@TOOL_VERSION@">482</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">24.2</token> + </macros> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">ucsc-mafcoverage</requirement> + </requirements> + <command detect_errors="exit_code"> + <![CDATA[ + cp '$ucsc_db_connection' "\${HOME}/.hg.conf" && + chmod 600 "\${HOME}/.hg.conf" && + mafCoverage + '$genome' + '$maf_file' + #if $restrict_option.restrict_select == "yes": + -restrict='$restrict_option.restrict_bed' + #end if + #if $count != "": + -count=$count + #end if + > coverage.txt + ]]> + </command> + <configfiles> + <configfile name="ucsc_db_connection"><![CDATA[ +#European MariaDB server +db.host=genome-euro-mysql.soe.ucsc.edu +db.user=genomep +db.password=password +central.db=hgcentral +central.host=genome-euro-mysql.soe.ucsc.edu +central.user=genomep +central.password=password +gbdbLoc1=http://hgdownload.soe.ucsc.edu/gbdb/ +forceTwoBit=on + ]]></configfile> + </configfiles> + <inputs> + <param name="maf_file" type="data" format="maf" label="Input MAF file" help="Input MAF file for which coverage needs to be analysed. MAF file must be sorted by chromosome, tStart"/> + <param name="genome" type="text" optional="false" label="Enter Genome database name" help="Name should match with the UCSC Table Browser Entries (For Eg. mm10, hg19, hg38)"/> + <conditional name="restrict_option"> + <param name="restrict_select" type="select" label="Restrict to a specific parts of input BED file" help="Restrict the MAF coverage to a specific part of the input BED file. If not selected, the entire BED file will be used."> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <when value="yes"> + <param name="restrict_bed" type="data" format="bed" label="Restrict BED file" help="Select a BED file to restrict the MAF coverage to specific regions."/> + </when> + <when value="no"/> + </conditional> + <param name="count" type="integer" value="" optional="true" label="Number of matching species to count coverage" help="Number of species to count coverage for. Default is 3"/> + </inputs> + <outputs> + <data name="output" format="txt" from_work_dir="coverage.txt" label="${tool.name} on ${on_string}:Output Coverage"/> + </outputs> + <tests> + <!-- Test 01: Testing with default options --> + <test expect_num_outputs="1"> + <param name="maf_file" value="mafFetch.maf"/> + <param name="genome" value="hg19"/> + <conditional name="restrict_option"> + <param name="restrict_select" value="no"/> + </conditional> + <output name="output" ftype="txt"> + <assert_contents> + <has_n_lines n="16"/> + <has_text_matching expression="all\t330\t0.00\t170\t0.00\t25\t0.00\t145\t0.00"/> + <has_text_matching expression="chr13\t214\t0.00\t101\t0.00\t17\t0.00\t84\t0.00"/> + <has_text_matching expression="chr17\t116\t0.00\t69\t0.00\t8\t0.00\t61\t0.00"/> + </assert_contents> + </output> + </test> + + <!-- Test 02: Testing -count option --> + <test expect_num_outputs="1"> + <param name="maf_file" value="mafFetch.maf"/> + <param name="genome" value="hg19"/> + <conditional name="restrict_option"> + <param name="restrict_select" value="no"/> + </conditional> + <param name="count" value="2"/> + <output name="output" ftype="txt"> + <assert_contents> + <has_n_lines n="16"/> + <has_text_matching expression="all\t330\t0.00\t170\t0.00\t25\t0.00\t145\t0.00"/> + <has_text_matching expression="chr13\t214\t0.00\t101\t0.00\t17\t0.00\t84\t0.00"/> + <has_text_matching expression="chr17\t116\t0.00\t69\t0.00\t8\t0.00\t61\t0.00"/> + </assert_contents> + </output> + </test> + + <!-- Test 03: Testing with restrict option --> + <test expect_num_outputs="1"> + <param name="maf_file" value="mafFetch.maf"/> + <param name="genome" value="hg19"/> + <conditional name="restrict_option"> + <param name="restrict_select" value="yes"/> + <param name="restrict_bed" value="restrict.bed"/> + </conditional> + <param name="count" value="3"/> + <output name="output" ftype="txt"> + <assert_contents> + <has_n_lines n="17"/> + <has_text_matching expression="all\t207\t94.09\t78\t35.45\t6\t2.73\t72\t32.73"/> + <has_text_matching expression="chr13\t107\t89.17\t16\t13.33\t0\t0.00\t16\t13.33"/> + <has_text_matching expression="chr17\t100\t100.00\t62\t62.00\t6\t6.00\t56\t56.00"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ + +mafCoverage is a command-line tool from the UCSC Genome Browser suite that analyses the coverage by MAF files chromosome by chromosome and genome-wide. + + ]]></help> + <citations> + <citation type="bibtex"> + @misc{mafCoverage, + author = {Kent UCSC}, + title = {mafCoverage: A tool for analysing coverage by MAF files chromosome by chromosome and genome-wide}, + note = {Tool for analysing coverage by MAF files chromosome by chromosome and genome-wide} + </citation> + </citations> + <creator> + <person givenName="Saim" familyName="Momin" url="https://github.com/SaimMomin12" identifier="https://orcid.org/0009-0003-9935-828X"/> + <organization name="Galaxy Europe" url="https://galaxyproject.org/eu/"/> + </creator> +</tool> \ No newline at end of file