dimspy_process_scans: macros.xml annotate

annotate macros.xml @ 0:62c4813fbe7a draft

"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"

author	computational-metabolomics
date	Sat, 11 Apr 2020 16:48:19 -0400
parents
children	deafa30d6570

rev	line source
0 62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	1 <macros>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	2 <token name="@TOOL_VERSION@">1.4.0</token>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	3 <token name="@GALAXY_TOOL_VERSION@">0</token>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	4
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	5 <xml name="requirements">
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	6 <requirements>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	7 <requirement type="package" version="@TOOL_VERSION@">dimspy</requirement>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	8 </requirements>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	9 </xml>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	10
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	11 <token name="@HDF5_PM_TO_TXT@">
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	12 dimspy hdf5-pm-to-txt
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	13 --input '$hdf5_file_out'
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	14 --output '$matrix_file_out'
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	15 --delimiter $delimiter
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	16 --attribute_name $hdf5_to_txt.matrix_attr
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	17 --representation-samples $hdf5_to_txt.representation_samples
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	18 </token>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	19
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	20 <token name="@HDF5_PM_TO_TXT_COMPREHENSIVE@">
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	21 dimspy hdf5-pm-to-txt
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	22 --input '$hdf5_file_out'
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	23 --output '$matrix_comprehensive_file_out'
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	24 --delimiter $delimiter
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	25 --comprehensive
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	26 --attribute_name $hdf5_to_txt.matrix_attr
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	27 --representation-samples $hdf5_to_txt.representation_samples
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	28 </token>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	29
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	30 <xml name="hdf5_pm_to_txt">
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	31 <section name="hdf5_to_txt" title="Show options for addtional output (*.tsv files)" expanded="False">
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	32 <param name="standard" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Standard output?" help="Set to "yes" to produce a "standard" Peak Matrix (i.e. m/z and intensity)."/>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	33 <param name="comprehensive" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Comprehensive output?" help="Set to "yes" to produce a Peak Matrix with additional information (e.g. m/z and intensity, rsd, missing values)."/>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	34 <param name="representation_samples" type="select" label="Should the rows or columns represent the samples?" help="">
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	35 <option value="rows" selected="true">Rows</option>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	36 <option value="columns">Columns</option>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	37 </param>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	38 <param name="matrix_attr" type="select" label="The Peak Matrix should contain ... values" help="">
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	39 <option value="intensity" selected="true">Intensity</option>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	40 <option value="mz">m/z</option>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	41 <option value="snr">Signal-to-noise ratio (SNR)</option>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	42 </param>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	43 </section>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	44 </xml>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	45
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	46 <xml name="outputs_peak_intensity_matrix">
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	47 <data name="hdf5_file_out" format="h5" label="${tool.name} on ${on_string}: Peak Intensity Matrix (HDF5 file)"/>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	48 <data name="matrix_file_out" format="tsv" label="${tool.name} on ${on_string}: Peak Intensity Matrix">
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	49 <filter>hdf5_to_txt["standard"] is True</filter>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	50 </data>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	51 <data name="matrix_comprehensive_file_out" format="tsv" label="${tool.name} on ${on_string}: Peak Intensity Matrix (comprehensive)" >
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	52 <filter>hdf5_to_txt["comprehensive"] is True</filter>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	53 </data>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	54 </xml>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	55
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	56 <xml name="citations">
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	57 <citations>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	58 <citation type="doi">10.1038/nprot.2016.156</citation>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	59 <citation type="doi">10.1038/sdata.2014.12</citation>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	60 <citation type="doi">10.1021/ac062446p</citation>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	61 <citation type="doi">10.1021/ac2001803</citation>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	62 <yield />
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	63 </citations>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	64 </xml>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	65
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	66 <token name="@example_filelist@"><![CDATA[
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	67
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	68 +-------------------------+----------------+---------------+-----------+--------------------+-----------+
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	69 \| filename \| classLabel \| replicate \| batch \| injectionOrder \| [...] \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	70 +-------------------------+----------------+---------------+-----------+--------------------+-----------+
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	71 \| sample_rep1.raw \| sample \| 1 \| 1 \| 1 \| [...] \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	72 +-------------------------+----------------+---------------+-----------+--------------------+-----------+
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	73 \| sample_rep2.raw \| sample \| 2 \| 1 \| 2 \| [...] \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	74 +-------------------------+----------------+---------------+-----------+--------------------+-----------+
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	75 \| sample_rep3.raw \| sample \| 3 \| 1 \| 3 \| [...] \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	76 +-------------------------+----------------+---------------+-----------+--------------------+-----------+
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	77 \| sample_rep4.raw \| sample \| 4 \| 1 \| 4 \| [...] \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	78 +-------------------------+----------------+---------------+-----------+--------------------+-----------+
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	79 \| blank_rep1.raw \| blank \| 1 \| 1 \| 5 \| [...] \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	80 +-------------------------+----------------+---------------+-----------+--------------------+-----------+
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	81 \| blank_rep2.raw \| blank \| 2 \| 1 \| 6 \| [...] \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	82 +-------------------------+----------------+---------------+-----------+--------------------+-----------+
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	83 \| blank_rep3.raw \| blank \| 3 \| 1 \| 7 \| [...] \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	84 +-------------------------+----------------+---------------+-----------+--------------------+-----------+
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	85 \| blank_rep4.raw \| blank \| 4 \| 1 \| 8 \| [...] \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	86 +-------------------------+----------------+---------------+-----------+--------------------+-----------+
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	87 \| ... \| ... \| ... \| ... \| ... \| [...] \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	88 +-------------------------+----------------+---------------+-----------+--------------------+-----------+
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	89
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	90 ]]></token>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	91
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	92
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	93 <token name="@help_columns_peaklist@">
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	94
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	95 - mz - the mass-to-charge ratio of the extracted mass spectral peak
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	96
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	97 - intensity - the intensity of the extracted mass spectral peak
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	98
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	99 - snr - the signal-to-noise ratio of the extracted peak, which is defined as the ratio of the peak’s intensity value to that of the background noise intensity value
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	100
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	101 - present - a numeric value greater than 0 that indicates the total number of scans at least one peak was detected in a given file
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	102
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	103 - fraction - a proportion ranging from 0 to 1 that indicates the total number of times a peak was detected in a given scan event type, divided by the total number of occurrences of that scan event type recorded in a given file.
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	104
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	105 - purity - a numeric value ranging from 0 to 1 that indicates the proportion of scans, for a given scan event type, that contained a single mass spectral peak following hierarchical clustering. A purity score less-than 1 indicates that in some proportion of scans, multiple peaks within a single scan were grouped together during the hierarchical clustering process.
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	106
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	107 - occurrence - a numeric value greater than 0 that indicates the total number of peaks that were observed across scans within the user-defined ppm error tolerance.
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	108
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	109 - snr_flag - a boolean value indicating whether to keep (“1”) or discard (“0”) a peak according to its signal-to-noise ratio value.
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	110
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	111 - fraction_flag - a boolean value indicating whether a peak should be kept or discarded according to the ratio of the number of scans in which it was detected, to the the number of scans in which it was not detected.
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	112
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	113 - flags - a boolean value indicating whether a peak should be retained or discarded based upon both its ‘snr_flag’ and ‘fraction_flag’ boolean values (if either is set to ‘0’ i.e. discard peak, then the ‘flags’ boolean should also be 0).
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	114
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	115 </token>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	116
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	117 <token name="@example_peaklist@">
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	118
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	119
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	120 Example of an processed and filtered peaklist:
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	121
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	122
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	123 +-----------+-----------+------+---------+----------+-------+------------+--------+----------+---------------+-------+
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	124 \| mz \| intensity \| snr \| present \| fraction \| rsd \| occurrence \| purity \| snr_flag \| fraction_flag \| flags \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	125 +-----------+-----------+------+---------+----------+-------+------------+--------+----------+---------------+-------+
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	126 \| 90.44000 \| 4744.0 \| 3.06 \| 1 \| 0.063 \| nan \| 1 \| 1 \| 1 \| 0 \| 0 \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	127 +-----------+-----------+------+---------+----------+-------+------------+--------+----------+---------------+-------+
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	128 \| 97.07380 \| 5423.6 \| 3.52 \| 1 \| 0.063 \| nan \| 1 \| 1 \| 1 \| 0 \| 0 \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	129 +-----------+-----------+------+---------+----------+-------+------------+--------+----------+---------------+-------+
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	130 \| 99.04180 \| 4105.8 \| 3.60 \| 1 \| 0.063 \| nan \| 1 \| 1 \| 1 \| 0 \| 0 \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	131 +-----------+-----------+------+---------+----------+-------+------------+--------+----------+---------------+-------+
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	132 \| 99.49800 \| 4775.7 \| 3.05 \| 1 \| 0.063 \| nan \| 1 \| 1 \| 1 \| 0 \| 0 \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	133 +-----------+-----------+------+---------+----------+-------+------------+--------+----------+---------------+-------+
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	134 \| 99.95020 \| 5657.8 \| 3.63 \| 1 \| 0.063 \| nan \| 1 \| 1 \| 1 \| 0 \| 0 \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	135 +-----------+-----------+------+---------+----------+-------+------------+--------+----------+---------------+-------+
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	136 \| 100.40660 \| 5489.5 \| 3.57 \| 3 \| 0.188 \| 14.51 \| 3 \| 1 \| 1 \| 0 \| 0 \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	137 +-----------+-----------+------+---------+----------+-------+------------+--------+----------+---------------+-------+
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	138 \| 100.8672 \| 4841.18 \| 3.27 \| 7 \| 0.4375 \| 16.36 \| 7 \| 1 \| 1 \| 0 \| 0 \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	139 +-----------+-----------+------+---------+----------+-------+------------+--------+----------+---------------+-------+
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	140 \| 101.0027 \| 9047.79 \| 5.99 \| 16 \| 1 \| 21.53 \| 19 \| 0.8125 \| 1 \| 1 \| 1 \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	141 +-----------+-----------+------+---------+----------+-------+------------+--------+----------+---------------+-------+
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	142 \| 101.0033 \| 271893.9 \| 182 \| 16 \| 1 \| 4.17 \| 16 \| 1 \| 1 \| 1 \| 1 \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	143 +-----------+-----------+------+---------+----------+-------+------------+--------+----------+---------------+-------+
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	144 \| 101.0038 \| 8738.03 \| 5.9 \| 14 \| 0.875 \| 9.71 \| 14 \| 1 \| 1 \| 1 \| 1 \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	145 +-----------+-----------+------+---------+----------+-------+------------+--------+----------+---------------+-------+
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	146 \| 101.004 \| 5166.67 \| 3.5 \| 5 \| 0.3125 \| 18.02 \| 6 \| 0.8 \| 1 \| 0 \| 0 \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	147 +-----------+-----------+------+---------+----------+-------+------------+--------+----------+---------------+-------+
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	148 \| 101.0599 \| 5894.69 \| 3.88 \| 2 \| 0.125 \| 15.06 \| 2 \| 1 \| 1 \| 0 \| 0 \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	149 +-----------+-----------+------+---------+----------+-------+------------+--------+----------+---------------+-------+
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	150 \| 101.2728 \| 6846.28 \| 4.44 \| 1 \| 0.0625 \| nan \| 1 \| 1 \| 1 \| 0 \| 0 \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	151 +-----------+-----------+------+---------+----------+-------+------------+--------+----------+---------------+-------+
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	152
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	153 </token>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	154
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	155 <token name="@help_options_addtional_output@">
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	156
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	157 Show options for additional output(s) (OPTIONAL):
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	158
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	159 - Standard output (default = No) - boolean toggle where selection of:
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	160
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	161 - No - prevent the export of a .txt formatted peak matrix to the active Galaxy history.
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	162
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	163 - Yes - export a .txt formatted peak matrix to the active Galaxy history that includes only those peaks from the input peak intensity matrix that passed the filtering procedure.
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	164
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	165 - Comprehensive output (default = "No") - boolean toggle where selection of:
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	166
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	167 - No - prevents export of a .txt formatted comprehensive peak matrix.
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	168
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	169 - Yes - exports a .txt formatted comprehensive peak matrix to the active Galaxy history that contains the m/z, missing values and other metrics associated with all peaks included in the input peak intensity matrix, including the metric defined by the "The peak matrix should contain intensity \| m/z \| SNR values" parameter.
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	170
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	171 - Should rows or columns represent the samples? (default = rows) - binary toggle where selection of:
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	172
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	173 - rows - sample information is presented in the rows and m/z values (for aligned mass spectral peaks) in the columns of any output peak matrix.
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	174
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	175 - columns - sample information is presented in the columns and m/z values (for aligned mass spectral peaks) in the rows of any output peak matrix.
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	176
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	177 - The peak matrix should contain intensity \| m/z \| SNR values - use this option to define which peak metric is inserted in to the cells of any optionally-output peak matrix:
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	178
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	179 - Intensity - writes the absolute peak intensity to the cells of the peak matrix
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	180
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	181 - m/z - writes the mass-to-charge ratio to the cells of the peak matrix
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	182
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	183 - signal-to-noise ratio (SNR) - writes the signal-to-noise ratio to the cells of the peak matrix
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	184
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	185 </token>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	186
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	187 <token name="@help_outputs_matrix@">
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	188
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	189 Default output - a HDF5 file containing the aligned peak intensity matrix.
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	190
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	191 \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	192
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	193 Optional outputs - the metric recorded in any optionally output peak matrix/matrices is defined using the parameter "The peak matrix should contain intensity \| m/z \| SNR values". By default, study samples are listed row-wise, while mass-to-charge ratios of the aligned mass spectral peaks are presented in columns (to adjust, users must adjust the "Should rows or columns represent samples" toggle to “columns”).
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	194
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	195
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	196 - Standard output - an aligned peak matrix in tab-delimited format (“.” as decimal and NA for missing values).
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	197
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	198 Example of a standard peak intensity matrix:
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	199
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	200 +------------+----------+----------+----------+----------+---------+
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	201 \| mz \| 96.04216 \| 99.08062 \| 100.0759 \| 100.8672 \| ... \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	202 +------------+----------+----------+----------+----------+---------+
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	203 \| QC_1 \| 0 \| 0 \| 0 \| 0 \| ... \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	204 +------------+----------+----------+----------+----------+---------+
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	205 \| Blank_1 \| 3342.626 \| 0 \| 0 \| 0 \| ... \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	206 +------------+----------+----------+----------+----------+---------+
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	207 \| Control_10 \| 0 \| 0 \| 45432.2 \| 0 \| ... \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	208 +------------+----------+----------+----------+----------+---------+
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	209 \| Sample_2 \| 0 \| 3423.3 \| 0 \| 0 \| ... \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	210 +------------+----------+----------+----------+----------+---------+
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	211 \| Control_5 \| 0 \| 0 \| 49759 \| 0 \| ... \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	212 +------------+----------+----------+----------+----------+---------+
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	213 \| Control_10 \| 0 \| \| 39890.5 \| 0 \| ... \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	214 +------------+----------+----------+----------+----------+---------+
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	215 \| Sample_20 \| 0 \| 14563.7 \| 0 \| 0 \| ... \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	216 +------------+----------+----------+----------+----------+---------+
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	217 \| Sample_2 \| 0 \| 34676.4 \| 0 \| 0 \| ... \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	218 +------------+----------+----------+----------+----------+---------+
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	219 \| Sample_14 \| 0 \| 13134.9 \| 0 \| 521.4 \| ... \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	220 +------------+----------+----------+----------+----------+---------+
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	221 \| ... \| ... \| ... \| ... \| ... \| ... \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	222 +------------+----------+----------+----------+----------+---------+
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	223
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	224 \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	225
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	226 - Comprehensive output - an aligned peak matrix, as described for the "standard output" (above), including all metadata from the "Process Scans" Filelist/samplelist and the following additional mass spectral peak metrics:
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	227
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	228 - present - a positive integer value (0 <![CDATA[ < ]]> value <![CDATA[ < ]]> total number of study samples in the filelist / samplelist) that indicates the total number of study samples in which a peak was detected with the specified mass-to-charge ratio, plus or minus the user-defined ppm error tolerance.
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	229
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	230 - occurrence - a positive integer value indicating the number of peaks that were grouped together during the alignment procedure and thus, that were used to calculate the average mass-to-charge ratio indicated for the aligned peak. A value greater than given in the “Present” metric indicates that one or more peaklists contained more-than one mass spectral peak with the specified mass-to-charge, plus or minus the user-defined ppm error tolerance.
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	231
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	232 - purity - a proportion ranging from 0 to 1 that indicates the number of scans in which only a single peak was detected during the peaklist alignment process. If the value in the “occurrence” metric is greater than the “present” metric, purity will be <![CDATA[ < ]]> 1. A purity <![CDATA[ < ]]> 1 means that in at least one peaklist there was more-than one mass spectral peak with the specified mass-to-charge, plus or minus the user-defined ppm error tolerance.
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	233
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	234 - rsd_all - a numeric value indicating the percent relative standard deviation (otherwise termed the percent coefficient of variation) of peak intensities for peaks aligned together using the Align Samples tool. If fewer than 2 peaks were aligned across samples, then the rsd_all column will be filled in with ‘nan’
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	235
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	236 - blank_flag (may be absent if "Blank filter” tool was not applied) - a boolean value where 0 = reject peak, 1 = accept peak. A peak is accepted during blank filtering if a user-defined minimum proportion of study samples had peak intensity values greater-than the product of the average of “reference” sample peak intensities and the “min_fold_change” parameter.
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	237
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	238 - fraction_flag (may be absent if "Sample filter” tool was not applied)- a boolean value where 0 = reject peak, 1 = accept peak. If greater-than a user-defined minimum fraction of samples (whether checked across ALL experimental classes, or within ANY of the individual experimental classes) had recorded intensity values for a given peak, then this peak is accepted, i.e. it is considered in downstream processing procedures, while rejected peaks are not.
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	239
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	240 - flags - a boolean value indicating whether a peak should be included (“1”) or excluded (“0”) from downstream processing procedures. Exclusion of a peak occurs if the thresholds for “relative standard deviation” and/or “minimum number of technical replicates a peak has to be present in” were not met.
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	241
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	242 \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	243
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	244 Example of a comprehensive peak intensity matrix:
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	245
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	246 +-------------+----------------+------------+-----------------+----------------+---------------------+-----------------+--------------+----------+----------+----------+----------+---------+
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	247 \| mz \| missing values \| tags_batch \| tags_replicates \| tags_replicate \| tags_injectionOrder \| tags_classLabel \| tags_untyped \| 96.04216 \| 99.08062 \| 100.0759 \| 100.8672 \| ... \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	248 +-------------+----------------+------------+-----------------+----------------+---------------------+-----------------+--------------+----------+----------+----------+----------+---------+
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	249 \| present* \| \| \| \| \| \| \| \| 1 \| 4 \| 3 \| 1 \| ... \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	250 +-------------+----------------+------------+-----------------+----------------+---------------------+-----------------+--------------+----------+----------+----------+----------+---------+
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	251 \| occurrence* \| \| \| \| \| \| \| \| 1 \| 4 \| 4 \| 1 \| ... \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	252 +-------------+----------------+------------+-----------------+----------------+---------------------+-----------------+--------------+----------+----------+----------+----------+---------+
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	253 \| purity* \| \| \| \| \| \| \| \| 1 \| 1 \| 1 \| 1 \| ... \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	254 +-------------+----------------+------------+-----------------+----------------+---------------------+-----------------+--------------+----------+----------+----------+----------+---------+
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	255 \| rsd_all* \| \| \| \| \| \| \| \| nan \| nan \| 10.98 \| nan \| ... \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	256 +-------------+----------------+------------+-----------------+----------------+---------------------+-----------------+--------------+----------+----------+----------+----------+---------+
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	257 \| flags* \| \| \| \| \| \| \| \| 1 \| 1 \| 1 \| 1 \| ... \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	258 +-------------+----------------+------------+-----------------+----------------+---------------------+-----------------+--------------+----------+----------+----------+----------+---------+
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	259 \| QC_1 \| 2901 \| 1 \| 2_3_4 \| 2 \| 2 \| QC \| \| 0 \| 0 \| 0 \| 0 \| ... \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	260 +-------------+----------------+------------+-----------------+----------------+---------------------+-----------------+--------------+----------+----------+----------+----------+---------+
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	261 \| Blank_1 \| 2948 \| 1 \| 1_2_4 \| 1 \| 5 \| Blank \| \| 3342.626 \| 0 \| 0 \| 0 \| ... \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	262 +-------------+----------------+------------+-----------------+----------------+---------------------+-----------------+--------------+----------+----------+----------+----------+---------+
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	263 \| Control_10 \| 2921 \| 1 \| 2_3_4 \| 2 \| 10 \| Control \| \| 0 \| 0 \| 45432.2 \| 0 \| ... \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	264 +-------------+----------------+------------+-----------------+----------------+---------------------+-----------------+--------------+----------+----------+----------+----------+---------+
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	265 \| Sample_2 \| 2819 \| 1 \| 1_2_4 \| 1 \| 13 \| Exposed \| \| 0 \| 3423.3 \| 0 \| 0 \| ... \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	266 +-------------+----------------+------------+-----------------+----------------+---------------------+-----------------+--------------+----------+----------+----------+----------+---------+
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	267 \| Control_5 \| 2877 \| 1 \| 2_3_4 \| 2 \| 18 \| Control \| \| 0 \| 0 \| 49759 \| 0 \| ... \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	268 +-------------+----------------+------------+-----------------+----------------+---------------------+-----------------+--------------+----------+----------+----------+----------+---------+
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	269 \| Control_10 \| 2856 \| 1 \| 1_2_3 \| 1 \| 21 \| Control \| \| 0 \| \| 39890.5 \| 0 \| ... \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	270 +-------------+----------------+------------+-----------------+----------------+---------------------+-----------------+--------------+----------+----------+----------+----------+---------+
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	271 \| Sample_20 \| 2855 \| 1 \| 1_2_4 \| 1 \| 25 \| Exposed \| \| 0 \| 14563.7 \| 0 \| 0 \| ... \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	272 +-------------+----------------+------------+-----------------+----------------+---------------------+-----------------+--------------+----------+----------+----------+----------+---------+
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	273 \| Sample_2 \| 2814 \| 1 \| 1_2_4 \| 1 \| 29 \| Exposed \| \| 0 \| 34676.4 \| 0 \| 0 \| ... \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	274 +-------------+----------------+------------+-----------------+----------------+---------------------+-----------------+--------------+----------+----------+----------+----------+---------+
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	275 \| Sample_14 \| 2870 \| 1 \| 1_2_3 \| 1 \| 33 \| Exposed \| \| 0 \| 13134.9 \| 0 \| 521.4 \| ... \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	276 +-------------+----------------+------------+-----------------+----------------+---------------------+-----------------+--------------+----------+----------+----------+----------+---------+
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	277 \| ... \| ... \| ... \| ... \| ... \| ... \| ... \| ... \| ... \| ... \| ... \| ... \| ... \|
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	278 +-------------+----------------+------------+-----------------+----------------+---------------------+-----------------+--------------+----------+----------+----------+----------+---------+
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	279
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	280 </token>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	281
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	282
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	283 <token name="@github_developers_contributors@">
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	284 Github respository (source code)
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	285 --------------------------------
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	286
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	287 Galaxy Tool Wrappers: https://github.com/computational-metabolomics/dimspy-galaxy/
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	288 DIMSpy package: https://github.com/computational-metabolomics/dimspy/
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	289
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	290
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	291 Developers and contributors
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	292 ---------------------------
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	293
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	294 - Ralf Weber (r.j.weber@bham.ac.uk) - University of Birmingham (UK)
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	295 - Martin R. Jones (m.r.jones.1@bham.ac.uk) - University of Birmingham (UK)
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	296 - Thomas Lawson (tnl495@bham.ac.uk) - University of Birmingham (UK)
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	297
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	298 </token>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	299
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	300 <token name="@license@">
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	301 License
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	302 -------
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	303 DIMSpy is released under the GNU General Public License v3.0 (see `LICENSE file`_)
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	304
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	305 .. _`LICENSE file`: https://github.com/computational-metabolomics/dimspy-galaxy/blob/master/LICENSE
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	306
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	307 </token>
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	308
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	309
62c4813fbe7a "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839" computational-metabolomics parents: diff changeset	310 </macros>

Mercurial > repos > computational-metabolomics > dimspy_process_scans

annotate macros.xml @ 0:62c4813fbe7a draft