Mercurial > repos > galaxyp > openms
diff SpectraMerger.xml @ 0:3070d71e0e5c draft
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author | bgruening |
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date | Thu, 16 Apr 2015 08:37:04 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SpectraMerger.xml Thu Apr 16 08:37:04 2015 -0400 @@ -0,0 +1,118 @@ +<?xml version='1.0' encoding='UTF-8'?> +<tool id="SpectraMerger" name="SpectraMerger" version="2.0.0"> + <description>Merges spectra (each MS level separately), increasing S/N ratios.</description> + <macros> + <token name="@EXECUTABLE@">SpectraMerger</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>SpectraMerger + +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +#if $param_merging_method: + -merging_method + #if " " in str($param_merging_method): + "$param_merging_method" + #else + $param_merging_method + #end if +#end if +-threads \${GALAXY_SLOTS:-24} + +#if $rep_param_algorithm_block_method_ms_levels: +-algorithm:block_method:ms_levels + #for token in $rep_param_algorithm_block_method_ms_levels: + #if " " in str(token): + "$token.param_algorithm_block_method_ms_levels" + #else + $token.param_algorithm_block_method_ms_levels + #end if + #end for +#end if +#if $param_algorithm_block_method_rt_block_size: + -algorithm:block_method:rt_block_size $param_algorithm_block_method_rt_block_size +#end if +#if $param_algorithm_block_method_rt_max_length: + -algorithm:block_method:rt_max_length $param_algorithm_block_method_rt_max_length +#end if +#if $param_algorithm_precursor_method_mz_tolerance: + -algorithm:precursor_method:mz_tolerance $param_algorithm_precursor_method_mz_tolerance +#end if +#if $param_algorithm_precursor_method_rt_tolerance: + -algorithm:precursor_method:rt_tolerance $param_algorithm_precursor_method_rt_tolerance +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if + #if $adv_opts.param_algorithm_mz_binning_width: + -algorithm:mz_binning_width $adv_opts.param_algorithm_mz_binning_width +#end if + #if $adv_opts.param_algorithm_mz_binning_width_unit: + -algorithm:mz_binning_width_unit + #if " " in str($adv_opts.param_algorithm_mz_binning_width_unit): + "$adv_opts.param_algorithm_mz_binning_width_unit" + #else + $adv_opts.param_algorithm_mz_binning_width_unit + #end if +#end if + #if $adv_opts.param_algorithm_sort_blocks: + -algorithm:sort_blocks + #if " " in str($adv_opts.param_algorithm_sort_blocks): + "$adv_opts.param_algorithm_sort_blocks" + #else + $adv_opts.param_algorithm_sort_blocks + #end if +#end if +#end if +</command> + <inputs> + <param name="param_in" type="data" format="mzml" optional="False" label="Input mzML file" help="(-in) "/> + <param name="param_merging_method" type="select" optional="True" value="block_method" label="Method of merging which should be used" help="(-merging_method) "> + <option value="precursor_method">precursor_method</option> + <option value="block_method">block_method</option> + </param> + <repeat name="rep_param_algorithm_block_method_ms_levels" min="0" max="1" title="param_algorithm_block_method_ms_levels"> + <param name="param_algorithm_block_method_ms_levels" type="text" min="1" optional="True" size="30" value="1" label="Merge spectra of this level" help="(-ms_levels) All spectra with other MS levels remain untouched"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + </repeat> + <param name="param_algorithm_block_method_rt_block_size" type="integer" min="1" optional="True" value="5" label="Maximum number of scans to be summed up" help="(-rt_block_size) "/> + <param name="param_algorithm_block_method_rt_max_length" type="float" min="0.0" max="1e+11" optional="True" value="0.0" label="Maximum RT size of the block in seconds (0.0 = no size restriction)" help="(-rt_max_length) "/> + <param name="param_algorithm_precursor_method_mz_tolerance" type="float" min="0.0" optional="True" value="0.0001" label="Max m/z distance of the precursor entries of two spectra to be merged in [Da]" help="(-mz_tolerance) "/> + <param name="param_algorithm_precursor_method_rt_tolerance" type="float" min="0.0" optional="True" value="5.0" label="Max RT distance of the precursor entries of two spectra to be merged in [s]" help="(-rt_tolerance) "/> + <expand macro="advanced_options"> + <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> + <param name="param_algorithm_mz_binning_width" type="float" min="0.0" optional="True" value="0.0001" label="Max m/z distance of two peaks to be merged" help="(-mz_binning_width) "/> + <param name="param_algorithm_mz_binning_width_unit" type="select" optional="True" value="Da" label="Unit in which the distance between two peaks is given" help="(-mz_binning_width_unit) "> + <option value="Da">Da</option> + <option value="ppm">ppm</option> + </param> + <param name="param_algorithm_sort_blocks" type="select" optional="True" value="RT_ascending" label="Sort blocks by <?> before merging them (useful for precursor order)" help="(-sort_blocks) "> + <option value="RT_ascending">RT_ascending</option> + <option value=" RT_descending"> RT_descending</option> + </param> + </expand> + </inputs> + <outputs> + <data name="param_out" format="mzml"/> + </outputs> + <help>**What it does** + +Merges spectra (each MS level separately), increasing S/N ratios. + + +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpectraMerger.html</help> + <expand macro="references"/> +</tool>