| Previous changeset 1:f700da3ba35f (2017-04-18) Next changeset 3:066cf4d993f5 (2017-08-09) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 50c26f7fbe8a2bd1347c860d7a62480865efc254 |
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modified:
IDFileConverter.xml readme.md |
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| diff -r f700da3ba35f -r 5588e443a7db IDFileConverter.xml --- a/IDFileConverter.xml Tue Apr 18 16:07:42 2017 -0400 +++ b/IDFileConverter.xml Thu Apr 27 13:23:15 2017 -0400 |
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| @@ -10,50 +10,59 @@ <expand macro="references"/> <expand macro="stdio"/> <expand macro="requirements"/> - <command>IDFileConverter + <command><![CDATA[ + + ## check input file type + #set $in_type = $param_in.ext + + ## create the symlinks to set the proper file extension, since IDFileConverter uses them to choose how to handle the input files + ln -s '$param_in' 'param_in.${in_type}' && + + IDFileConverter -#if $param_in: - -in $param_in -#end if -#if $param_out: - -out $param_out -#end if -#if $param_out_type: - -out_type - #if " " in str($param_out_type): - "$param_out_type" - #else - $param_out_type + #if $param_in: + -in 'param_in.${in_type}' + #end if + #if $param_out: + -out $param_out + #end if + #if $param_out_type: + -out_type + #if " " in str($param_out_type): + "$param_out_type" + #else + $param_out_type + #end if + #end if + #if $param_mz_file: + -mz_file $param_mz_file #end if -#end if -#if $param_mz_file: - -mz_file $param_mz_file -#end if -#if $param_mz_name: - -mz_name "$param_mz_name" -#end if -#if $param_peptideprophet_analyzed: - -peptideprophet_analyzed -#end if -#if $param_score_type: - -score_type - #if " " in str($param_score_type): - "$param_score_type" - #else - $param_score_type + #if $param_mz_name: + -mz_name "$param_mz_name" + #end if + #if $param_peptideprophet_analyzed: + -peptideprophet_analyzed #end if -#end if -#if $adv_opts.adv_opts_selector=='advanced': - #if $adv_opts.param_ignore_proteins_per_peptide: - -ignore_proteins_per_peptide -#end if - #if $adv_opts.param_scan_regex: - -scan_regex "$adv_opts.param_scan_regex" -#end if - #if $adv_opts.param_force: - -force -#end if -#end if + #if $param_score_type: + -score_type + #if " " in str($param_score_type): + "$param_score_type" + #else + $param_score_type + #end if + #end if + #if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_ignore_proteins_per_peptide: + -ignore_proteins_per_peptide + #end if + #if $adv_opts.param_scan_regex: + -scan_regex "$adv_opts.param_scan_regex" + #end if + #if $adv_opts.param_force: + -force + #end if + #end if + ]]> </command> <inputs> <param name="param_in" type="data" format="tabular,mzid,pepxml,idxml" optional="False" label="Input file or directory containing the data to convert" help="(-in) This may be: <br>- a single file in a multi-purpose XML format (pepXML, protXML, idXML, mzid), <br>- a single file in a search engine-specific format (Mascot: mascotXML, OMSSA: omssaXML, X! Tandem: xml, Percolator: psms), <br>- a single text file (tab separated) with one line for all peptide sequences matching a spectrum (top N hits), <br>- for Sequest results, a directory containing .out files. <br>"/> @@ -92,7 +101,7 @@ </expand> </inputs> <outputs> - <data name="param_out" format="mzid"/> + <data name="param_out" auto_format="true"/> </outputs> <help>Converts identification engine file formats. |
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| diff -r f700da3ba35f -r 5588e443a7db readme.md --- a/readme.md Tue Apr 18 16:07:42 2017 -0400 +++ b/readme.md Thu Apr 27 13:23:15 2017 -0400 |
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| @@ -102,10 +102,32 @@ [...] ]]> ``` + + * In `IDFileConverter.xml` the following is needed in the command section at the beginning (check your file to know what to copy where): + + ``` + <command><![CDATA[ + + ## check input file type + #set $in_type = $param_in.ext - * In `FileConverter.xml` add `auto_format="true"` to the output, e.g.: + ## create the symlinks to set the proper file extension, since IDFileConverter uses them to choose how to handle the input files + ln -s '$param_in' 'param_in.${in_type}' && + + IDFileConverter + + #if $param_in: + -in 'param_in.${in_type}' + #end if + + [...] + ]]> + ``` + + * In `IDFileConverter.xml` and `FileConverter.xml` add `auto_format="true"` to the output, e.g.: - <data name="param_out" metadata_source="param_in" auto_format="true"/> + - `<data name="param_out" auto_format="true"/>` + - `<data name="param_out" metadata_source="param_in" auto_format="true"/>` * To add an example test case to `DecoyDatabase.xml` add the following after the output section. If standard settings change you might have to adjust the options and/or the test files. |