Mercurial > repos > galaxyp > msgfplus
diff msgfplus.xml @ 4:58f9cf0de6d4 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus commit b2712071afd2d74261bc3e3fc555355f5675a0d6
| author | galaxyp |
|---|---|
| date | Wed, 23 Aug 2017 05:47:29 -0400 |
| parents | b4ccaf21855d |
| children | ce4882b95b73 |
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--- a/msgfplus.xml Thu Jan 12 15:25:02 2017 -0500 +++ b/msgfplus.xml Wed Aug 23 05:47:29 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="msgfplus" name="MS-GF+" version="0.1"> +<tool id="msgfplus" name="MS-GF+" version="0.2"> <description> Identifies peptides in tandem mass spectra using the MS-GF+ search engine. </description> @@ -14,17 +14,17 @@ <![CDATA[ #if $msgf_input.intype_selector == "single" - #set $db_name = $msgf_input.d.display_name.replace(".fasta", "") + ".fasta" - #set $input_name = $msgf_input.s.display_name + #set $db_name = $msgf_input.d.element_identifier.replace(".fasta", "") + ".fasta" + #set $input_name = $msgf_input.s.element_identifier.replace(".mzML", "") + ".mzML" ln -s '$msgf_input.s' '${input_name}' && ln -s '$msgf_input.d' '${db_name}' && #else if $msgf_input.intype_selector == "fractions" - #set $db_name = $msgf_input.db_spectra.reverse.display_name.replace(".fasta", "") + ".fasta" - #set $input_name = $msgf_input.db_spectra.forward.display_name + #set $db_name = $msgf_input.db_spectra.reverse.element_identifier.replace(".fasta", "") + ".fasta" + #set $input_name = $msgf_input.db_spectra.forward.element_identifier.replace(".mzML", "") + ".mzML" ln -s '$msgf_input.db_spectra.forward' '${input_name}' && ln -s '$msgf_input.db_spectra.reverse' '${db_name}' && #end if - #set $output_name = $input_name.replace(".mzML", "") + ".mzid" + #set $output_name = $input_name.replace(".mzML", ".mzid") echo \\#Mods > Mods.txt && #set $common_mods = str($common_fixed_modifications) + "," + str($common_variable_modifications) @@ -78,7 +78,7 @@ </when> <when value="fractions"> <param name="db_spectra" type="data_collection" collection_type="paired" - label="Collection: Pairs of FASTA database (forward) and spectra (reverse)"/> + label="Collection: Pairs of spectra (forward) and FASTA database (reverse)"/> </when> </conditional> <param name="tsvcheck" type="boolean" label="Output TSV as well?" /> @@ -269,7 +269,7 @@ <param name="precursor_ion_tol_units" value="ppm" /> <param name="common_fixed_modifications" value="" /> <param name="common_variable_modifications" value="" /> - <output name="output" file="201208-378803-msgf_20161026-50ppm-semitryptic-no_mods.mzid" compare="sim_size" delta="20" /> + <output name="output" file="201208-378803-msgf_20161026-50ppm-semitryptic-no_mods.mzid" compare="sim_size" delta="100" /> </test> <test> <param name="msgf_input|intype_selector" value="single" />