| Next changeset 1:6278dd24a860 (2021-04-08) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit d94002fc79f552c8a64ffca86298396b1568df97" |
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added:
encyclopedia_library_to_blib.xml macros.xml static/images/SearchToLib_Workflow.png |
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| diff -r 000000000000 -r 0202b8f3a516 encyclopedia_library_to_blib.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/encyclopedia_library_to_blib.xml Mon Sep 14 17:07:04 2020 +0000 |
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| @@ -0,0 +1,43 @@ +<tool id="encyclopedia_library_to_blib" name="ConvertLibraryToBlib" version="@VERSION@.0" python_template_version="3.5"> + <description>Convert EncyclopeDIA Library to BLIB for Skyline</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="aggressive"><![CDATA[ + EncyclopeDIA -convert -libtoblib + -Djava.awt.headless=true -Duser.language=en-US -Duser.region=US + -Xmx\$[ \${GALAXY_MEMORY_MB:-20480} / 1024 ]g + -numberOfThreadsUsed "\${GALAXY_SLOTS:-4}" + -i '$i' + -o '$output' + #if $istest == 'yes' + && sqlite3 -readonly '$output' 'SELECT distinct peptideSeq FROM RefSpectra;' > '$test_output' + #end if + ]]></command> + <inputs> + <param argument="-i" type="data" format="elib,dlib" label="Library: Chromatagram .ELIB or Spectrum .DLIB"/> + <param name="istest" type="hidden" value="no"/> + </inputs> + <outputs> + <data name="output" format="blib" label="${i.name} blib"/> + <data name="test_output" format="txt" > + <filter>istest == 'yes'</filter> + </data> + </outputs> + <tests> + <test> + <param name="i" ftype="dlib" value="PrositLib.dlib"/> + <param name="istest" value="yes"/> + <output name="test_output" ftype="txt"> + <assert_contents> + <has_text text="AGGVLHDDENLWSFGK"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ + Convert EncyclopeDIA Library to BLIB for Skyline. + ]]></help> + <expand macro="citations" /> +</tool> |
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| diff -r 000000000000 -r 0202b8f3a516 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Sep 14 17:07:04 2020 +0000 |
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| b'@@ -0,0 +1,551 @@\n+<macros>\n+ <token name="@VERSION@">0.9.5</token>\n+ <xml name="requirements">\n+ <requirements>\n+ <requirement type="package" version="@VERSION@">encyclopedia</requirement>\n+ <yield/>\n+ </requirements>\n+ </xml>\n+\n+ <token name="@ENCYCLOPEDIA_WIKI@">\n+EncyclopeDIA_ is library search engine comprised of several algorithms for DIA data analysis and can search for peptides using either DDA-based spectrum libraries or DIA-based chromatogram libraries. See: https://bitbucket.org/searleb/encyclopedia/wiki/Home\n+\n+.. _EncyclopeDIA: https://bitbucket.org/searleb/encyclopedia/wiki/Home\n+ </token>\n+ <xml name="citations">\n+ <citations>\n+ <citation type="doi">10.1038/s41467-018-07454-w</citation>\n+ <citation type="doi">10.1038/s41467-020-15346-1</citation>\n+ <citation type="doi">10.1074/mcp.P119.001913</citation>\n+ <yield/>\n+ </citations>\n+ </xml>\n+\n+ <token name="@CMD_IMPORTS@">\n+#import re\n+#def identifier_or_name($input1)\n+ #if hasattr($input1, \'element_identifier\')\n+ #return $input1.element_identifier\n+ #else\n+ #return $input1.name\n+ #end if\n+#end def\n+#def clean($name1)\n+ #set $name_clean = $re.sub(\'[^\\w\\-_]\', \'_\', $re.sub(\'(?i)[.](fa|fasta|imzml|mzml)$\',\'\', $re.sub(\'.*/\',\'\', $name1.rstrip(\'.gz\'))))\n+ #return $name_clean\n+#end def\n+#def ln_name($ds) \n+ #set $ext = \'\'\n+ #if $ds.is_of_type(\'mzml\') or $ds.is_of_type(\'imzml\')\n+ #set $ext = ".mzML"\n+ #else if $ds.is_of_type(\'elib\')\n+ #set $ext = ".elib"\n+ #else if $ds.is_of_type(\'dlib\')\n+ #set $ext = ".dlib"\n+ #else if $ds.is_of_type(\'blib\')\n+ #set $ext = ".blib"\n+ #else if $ds.is_of_type(\'fasta\')\n+ #set $ext = ".fasta"\n+ #else if $ds.is_of_type(\'fasta.gz\')\n+ #set $ext = ".fasta.gz"\n+ #end if\n+ #set $name = "%s%s" % ($clean($identifier_or_name($ds)),$ext) \n+ #return $name\n+#end def\n+#set $i_name = None\n+#set $f_name = None\n+#set $l_name = None\n+#set $t_name = None\n+ </token>\n+\n+ <xml name="scan_input">\n+ <param name="scan_input" argument="-i" type="data" format="imzml,mzml" label="Spectrum file in mzML format"> \n+ <help>@MSCONVERT_RAW@</help>\n+ </param>\n+ </xml>\n+ <token name="@LINK_SCAN_INPUT@"><![CDATA[\n+ #set $i_name = $ln_name($scan_input)\n+ ln -s \'$scan_input\' \'$i_name\' &&\n+ ]]></token>\n+ <token name="@SCAN_INPUT@">\n+ -i \'$i_name\'\n+ </token>\n+\n+ <xml name="scan_inputs">\n+ <param name="scan_inputs" argument="-i" type="data" format="imzml,mzml" multiple="true" label="Spectrum files in mzML format">\n+ <help>@MSCONVERT_RAW@</help>\n+ </param>\n+ </xml>\n+ <token name="@LINK_SCAN_INPUTS@"><![CDATA[\n+ #set $inputs_dir = \'inputs\'\n+ mkdir -p $inputs_dir &&\n+ #for $sf in $scan_inputs\n+ #set $i_name = $ln_name($sf)\n+ ln -s \'$sf\' \'${inputs_dir}/${i_name}\' &&\n+ #end for\n+ ]]></token>\n+ <token name="@SCAN_INPUTS@">\n+ -i \'$inputs_dir\'\n+ </token>\n+\n+ <xml name="fasta_input">\n+ <param name="fasta" argument="-f" type="data" format="fasta" label="Background proteome protein fasta database"> \n+ <help>provides the necessary peptide-to-protein links not specified in the spectrum library</help>\n+ </param>\n+ </xml>\n+ <token name="@LINK_FASTA_INPUT@"><![CDATA[\n+ #set $f_name = $ln_name($fasta)\n+ ln -s \'$fasta\' \'$f_name\' &&\n+ ]]></token>\n+ <token name="@FASTA_INPUT@">\n+ -f \'$f_name\'\n+ </token>\n+\n+ <xml name="target_fasta">\n+ <param name="target_fasta" argument="-t" type="data" format="fasta" label="Target fasta database" optional="true"> \n+ <help>Optional - Only analyze this subset of the background fasta proteome</help>\n+ </param>\n+ <param argument="-tp" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Target FASTA file contains peptides">\n+ '..b' <param argument="-numberOfQuantitativePeaks" type="integer" value="3" min="1" max="10" label="numberOfQuantitativePeaks" optional="true"/>\n+<!--\n+ <param argument="-addDecoysToBackground" type="boolean" truevalue="true" falsevalue="false" checked="false" label="addDecoysToBackground"/>\n+ <param argument="-dontRunDecoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="dontRunDecoys"/>\n+-->\n+ </when>\n+ </conditional>\n+ </xml>\n+ <token name="@SEARCH_OPTIONS@">\n+ #if $options.search.set_search == \'yes\'\n+ -minCharge $options.search.minCharge\n+ -maxCharge $options.search.maxCharge\n+ -minLength $options.search.minLength\n+ -maxLength $options.search.maxLength\n+ -minEluteTime $options.search.minEluteTime\n+ -maxMissedCleavage $options.search.maxMissedCleavage\n+ -minQuantitativeIonNumber $options.search.minQuantitativeIonNumber\n+ -minNumOfQuantitativePeaks $options.search.minNumOfQuantitativePeaks\n+ -numberOfQuantitativePeaks $options.search.numberOfQuantitativePeaks\n+ ## -addDecoysToBackground $options.search.addDecoysToBackground\n+ ## -dontRunDecoys $options.search.dontRunDecoys\n+ #end if\n+ </token>\n+\n+ <xml name="options_section">\n+ <section name="options" title="Parameter Settings" expanded="false">\n+ <expand macro="common_options"/>\n+ <expand macro="mass_library_tolerance"/>\n+ <expand macro="percolator_options"/>\n+ <expand macro="peak_options"/>\n+ <expand macro="window_options"/>\n+ <expand macro="modification_options"/>\n+ <expand macro="search_options"/>\n+ </section>\n+ </xml>\n+\n+ <xml name="libexport">\n+ <param argument="-a" type="boolean" truevalue="true" falsevalue="false" checked="false" label="align between files"/>\n+ </xml>\n+\n+ <token name="@SEARCH2LIB_CMDS@"><![CDATA[\n+ @CMD_IMPORTS@\n+ @LINK_SCAN_INPUTS@\n+ @LINK_FASTA_INPUT@\n+ @LINK_TARGET_FASTA@\n+ @LINK_LIB_INPUT@\n+ for SCAN_FILE in `ls -1 inputs/*`; do\n+ echo "\\$SCAN_FILE" &&\n+ EncyclopeDIA -Djava.awt.headless=true -Duser.language=en-US -Duser.region=US\n+ -Xmx\\$[ \\${GALAXY_MEMORY_MB:-20480} / 1024 ]g\n+ -numberOfThreadsUsed "\\${GALAXY_SLOTS:-4}"\n+ #if not $library\n+ -walnut\n+ #end if\n+ -i \\$SCAN_FILE\n+ @FASTA_INPUT@\n+ @TARGET_FASTA@\n+ @LIB_INPUT@\n+ @COMMON_OPTIONS@\n+ @MASS_LIBRARY_TOLERANCE@\n+ @PERCOLATOR_OPTIONS@\n+ @PEAK_OPTIONS@\n+ @WINDOW_OPTIONS@\n+ @MODIFICATION_OPTIONS@\n+ @SEARCH_OPTIONS@ | tee -a search2lib.log\n+ ; done &&\n+ for TXT in `find inputs/*.mzML.[efw]*[ast].txt`; do TRGT=`echo \\$TXT | sed \'s/mzML/dia/\'`; ln -s \\$TXT \\$TRGT; done &&\n+ EncyclopeDIA -Djava.awt.headless=true -Duser.language=en-US -Duser.region=US -Xmx\\$[ \\${GALAXY_MEMORY_MB:-20480} / 1024 ]g -libexport\n+ #if not $library\n+ -pecan\n+ #end if\n+ @SCAN_INPUTS@\n+ @FASTA_INPUT@\n+ @TARGET_FASTA@\n+ @LIB_INPUT@\n+ -a $a\n+ -o chromatogram_library.elib\n+ && ls -l ./*.* inputs/*\n+ | tee -a search2lib.log\n+]]>\n+ </token>\n+ <token name="@MSCONVERT_CMD@"><![CDATA[\n+ msconvert --zlib --64 --mzML --simAsSpectra --filter "peakPicking true 1-" --filter "demultiplex optimization=overlap_only" *.raw\n+]]>\n+ </token>\n+ <token name="@MSCONVERT_RAW@"><![CDATA[\n+mzML conversion from RAW requires special options: @MSCONVERT_CMD@\n+]]>\n+ </token>\n+ <token name="@MSCONVERT_HELP@"><![CDATA[\n+\n+ The MSConvert command can be used to convert and deconvolute DIA raw files to mzML format. You need to use these options:\n+\n+ ::\n+\n+ @MSCONVERT_CMD@\n+\n+]]>\n+ </token>\n+</macros>\n' |
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| diff -r 000000000000 -r 0202b8f3a516 static/images/SearchToLib_Workflow.png |
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| Binary file static/images/SearchToLib_Workflow.png has changed |
