Mercurial > repos > jjohnson > encyclopedia_prosit_csv_to_library
diff macros.xml @ 5:bd7ce1544554 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 880d327a6dce00616a0b0b58bcabcea7b58358cc"
author | jjohnson |
---|---|
date | Wed, 19 Aug 2020 08:37:37 -0400 |
parents | 602d01de42b4 |
children | d742ebf29341 |
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--- a/macros.xml Tue Jul 07 11:56:02 2020 -0400 +++ b/macros.xml Wed Aug 19 08:37:37 2020 -0400 @@ -59,27 +59,27 @@ </token> <xml name="scan_input"> - <param argument="-i" type="data" format="imzml,mzml" label="Spectrum file in mzML format"> + <param name="scan_input" argument="-i" type="data" format="imzml,mzml" label="Spectrum file in mzML format"> <help>@MSCONVERT_RAW@</help> </param> </xml> <token name="@LINK_SCAN_INPUT@"><![CDATA[ - #set $i_name = $ln_name($i) - ln -s '$i' '$i_name' && + #set $i_name = $ln_name($scan_input) + ln -s '$scan_input' '$i_name' && ]]></token> <token name="@SCAN_INPUT@"> -i '$i_name' </token> <xml name="scan_inputs"> - <param argument="-i" type="data" format="imzml,mzml" multiple="true" label="Spectrum files in mzML format"> + <param name="scan_inputs" argument="-i" type="data" format="imzml,mzml" multiple="true" label="Spectrum files in mzML format"> <help>@MSCONVERT_RAW@</help> </param> </xml> <token name="@LINK_SCAN_INPUTS@"><![CDATA[ #set $inputs_dir = 'inputs' mkdir -p $inputs_dir && - #for $sf in $i + #for $sf in $scan_inputs #set $i_name = $ln_name($sf) ln -s '$sf' '${inputs_dir}/${i_name}' && #end for @@ -89,26 +89,26 @@ </token> <xml name="fasta_input"> - <param argument="-f" type="data" format="fasta" label="Background proteome protein fasta database"> + <param name="fasta" argument="-f" type="data" format="fasta" label="Background proteome protein fasta database"> <help>provides the necessary peptide-to-protein links not specified in the spectrum library</help> </param> </xml> <token name="@LINK_FASTA_INPUT@"><![CDATA[ - #set $f_name = $ln_name($f) - ln -s '$f' '$f_name' && + #set $f_name = $ln_name($fasta) + ln -s '$fasta' '$f_name' && ]]></token> <token name="@FASTA_INPUT@"> -f '$f_name' </token> <xml name="target_fasta"> - <param argument="-t" type="data" format="fasta" label="Target fasta database" optional="true"/> + <param name="target_fasta" argument="-t" type="data" format="fasta" label="Target fasta database" optional="true"/> <param argument="-tp" type="boolean" truevalue="true" falsevalue="false" checked="false" label="target FASTA file contains peptides"/> </xml> <token name="@LINK_TARGET_FASTA@"><![CDATA[ - #if $t - #set $t_name = $ln_name($t) - ln -s '$t' '$t_name' && + #if $target_fasta + #set $t_name = $ln_name($target_fasta) + ln -s '$target_fasta' '$t_name' && #else #set $t_name = None #end if @@ -121,14 +121,14 @@ </token> <xml name="lib_input" token_optional="true" token_libhelp=""> - <param argument="-l" type="data" format="elib,dlib" optional="@OPTIONAL@" label="Library: Chromatagram .ELIB or Spectrum .DLIB"> + <param name="library" argument="-l" type="data" format="elib,dlib" optional="@OPTIONAL@" label="Library: Chromatagram .ELIB or Spectrum .DLIB"> <help>@LIBHELP@</help> </param> </xml> <token name="@LINK_LIB_INPUT@"><![CDATA[ - #if $l - #set $l_name = $ln_name($l) - cp '$l' $l_name && + #if $library + #set $l_name = $ln_name($library) + cp '$library' $l_name && #else #set $l_name = None #end if