Mercurial > repos > computational-metabolomics > dimspy_hdf5_to_txt

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"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
author computational-metabolomics
date Sat, 11 Apr 2020 16:45:45 -0400
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5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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1 <tool id="dimspy_hdf5_to_txt" name="Convert DIMSpy-based HDF5 to tsv" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@">
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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2 <description></description>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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3 <macros>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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4 <import>macros.xml</import>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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5 </macros>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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6 <expand macro="requirements" />
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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7 <command detect_errors="exit_code">
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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8 <![CDATA[
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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9 #if $input.object_type == 'peak_lists'
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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10 dimspy hdf5-pls-to-txt
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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11 --input '$input.hdf5_file_in'
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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12 --output .
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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13 --delimiter $delimiter
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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14 #elif $input.object_type == 'peak_matrix'
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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15 #if $input.matrix_format == 'standard' or $input.matrix_format == 'standard_comprehensive'
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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16 dimspy hdf5-pm-to-txt
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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17 --input '$input.hdf5_file_in'
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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18 --output '$matrix_file_out'
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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19 --delimiter $delimiter
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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20 --attribute_name $input.matrix_attr
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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21 --representation-samples $input.representation_samples
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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22 #end if
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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23 #if $input.matrix_format == "standard_comprehensive"
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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24 &&
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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25 #end if
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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26 #if $input.matrix_format == 'comprehensive' or $input.matrix_format == 'standard_comprehensive'
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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27 dimspy hdf5-pm-to-txt
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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28 --input '$input.hdf5_file_in'
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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29 --output '$matrix_comprehensive_file_out'
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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30 --delimiter $delimiter
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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31 --comprehensive
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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32 --attribute_name '$input.matrix_attr'
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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33 --representation-samples $input.representation_samples
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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34 #end if
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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35 #end if
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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36 ]]>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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37 </command>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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38 <inputs>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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39 <param name="delimiter" argument="--delimiter" type="hidden" value="tab" />
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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40 <conditional name="input">
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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41 <param name="object_type" type="select" label="Content HDF5 file" help="">
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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42 <option value="peak_matrix" selected="true">Peak Intensity Matrix</option>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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43 <option value="peak_lists">Peak list(s)</option>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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44 </param>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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45 <when value="peak_lists">
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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46 <param name="hdf5_file_in" argument="--input" type="data" format="h5" label="Peaklist(s) (HDF5 file)" help="" />
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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47 </when>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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48 <when value="peak_matrix">
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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49 <param name="hdf5_file_in" argument="--input" type="data" format="h5" label="Peak intensity matrix (HDF5 file)" help="" />
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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50 <param name="matrix_format" type="select" label="Select format(s) tsv formatted peak instensity matrix" help="">
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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51 <option value="standard" selected="true">Standard Peak Matrix (i.e. m/z and intensity).</option>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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52 <option value="comprehensive">Comprehensive Peak Matrix (e.g. m/z and intensity, rsd, missing values).</option>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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53 <option value="standard_comprehensive">Standard and comprehensive</option>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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54 </param>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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55 <param name="representation_samples" type="select" label="Should the rows or columns represent the samples?" help="">
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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56 <option value="rows" selected="true">Rows</option>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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57 <option value="columns">Columns</option>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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58 </param>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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59 <param name="matrix_attr" type="select" label="The Peak Matrix should contain ... values" help="">
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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60 <option value="intensity" selected="true">Intensity</option>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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61 <option value="mz">m/z</option>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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62 <option value="snr">Signal-to-noise ratio (SNR)</option>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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63 </param>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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64 </when>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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65 </conditional>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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66 </inputs>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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67 <outputs>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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68 <collection name="peaklists_txt" type="list" label="${tool.name} on ${on_string}: Peaklists">
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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69 <filter>input["object_type"] == "peak_lists"</filter>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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70 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" format="tsv" directory="." visible="false" />
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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71 </collection>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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72 <data name="matrix_file_out" format="tsv" label="${tool.name} on ${on_string}: Peak Matrix">
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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73 <filter>input["object_type"] == "peak_matrix" and (input["matrix_format"] == "standard" or input["matrix_format"] == "standard_comprehensive")</filter>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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74 </data>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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75 <data name="matrix_comprehensive_file_out" format="tsv" label="${tool.name} on ${on_string}: Peak Matrix (comprehensive)" >
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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76 <filter>input["object_type"] == "peak_matrix" and (input["matrix_format"] == "comprehensive" or input["matrix_format"] == "standard_comprehensive")</filter>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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77 </data>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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78 </outputs>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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79 <tests>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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80 <test>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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81 <conditional name="input">
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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82 <param name="object_type" value="peak_lists"/>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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83 <param name="hdf5_file_in" value="pls.h5" ftype="h5"/>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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84 </conditional>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
85 <output_collection name="peaklists_txt" type="list">
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
86 <element name="batch04_QC17_rep01_262" file="batch04_QC17_rep01_262.txt" ftype="tsv"/>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
87 <element name="batch04_QC17_rep02_263" file="batch04_QC17_rep02_263.txt" ftype="tsv"/>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
diff changeset
88 <element name="batch04_QC17_rep03_264" file="batch04_QC17_rep03_264.txt" ftype="tsv"/>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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89 </output_collection>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
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90 </test>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
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91 <test>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
parents:
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92 <conditional name="input">
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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93 <param name="object_type" value="peak_matrix"/>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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diff changeset
94 <param name="hdf5_file_in" value="pm_as_bf_sf.h5" ftype="h5"/>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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95 <param name="matrix_format" value="comprehensive"/>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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96 <param name="representation_samples" value="columns"/>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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97 <param name="matrix_attr" value="intensity"/>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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98 </conditional>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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99 <output name="matrix_comprehensive_file_out" file="peak_matrix_hdf5_to_txt_intensity.txt" ftype="tsv"/>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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100 </test>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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101 <test>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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102 <conditional name="input">
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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103 <param name="object_type" value="peak_matrix"/>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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104 <param name="hdf5_file_in" value="pm_as_bf_sf.h5" ftype="h5"/>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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105 <param name="matrix_format" value="standard"/>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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106 <param name="representation_samples" value="rows"/>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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107 <param name="matrix_attr" value="mz"/>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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108 </conditional>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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109 <output name="matrix_file_out" file="peak_matrix_hdf5_to_txt_mz.txt" ftype="tsv"/>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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110 </test>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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111 <test>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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112 <conditional name="input">
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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113 <param name="object_type" value="peak_matrix"/>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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114 <param name="hdf5_file_in" value="pm_as_bf_sf.h5" ftype="h5"/>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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115 <param name="matrix_format" value="standard_comprehensive"/>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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116 <param name="representation_samples" value="rows"/>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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117 <param name="matrix_attr" value="snr"/>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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118 </conditional>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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119 <output name="matrix_file_out" file="peak_matrix_hdf5_to_txt_snr.txt" ftype="tsv"/>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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120 <output name="matrix_comprehensive_file_out" file="peak_matrix_hdf5_to_txt_comprehensive_snr.txt" ftype="tsv"/>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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121 </test>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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122 </tests>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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123 <help>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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124 --------------------------------
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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125 Convert DIMSpy-based HDF5 to tsv
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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126 --------------------------------
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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127
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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128 ..
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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129
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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130 ----------------------------------
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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131
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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132 Description
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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133 -----------
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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134
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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135 This tool converts a .hdf5 file, containing either peaklist(s) or a peak intensity matrix, to user-friendly .tsv file(s).
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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136
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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137 ----------------------------------
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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138
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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139 Parameters
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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140 ----------
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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141
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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142 **Contents of hdf5 file** (REQUIRED; default = **peak intensity matrix**) - selection menu in which the user defines whether the input .hdf5 file contains:
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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143
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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144 - **a peak intensity matrix**
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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145
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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146 - **peaklist(s)**
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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147
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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148 |
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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149
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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150 **Peak intensity matrix or peaklists (HDF5 file)** (REQUIRED) - selection menu in which the user chooses the .hdf5 file (from the active Galaxy history) to be converted to .tsv formatted output(s).
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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151
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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152 |
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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153
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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154 **Select format(s) tsv formatted peak intensity matrix** (REQUIRED; default = **Standard Peak Matrix**) - selection menu in which the user chooses from the following export options:
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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155
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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156 @help_options_addtional_output@
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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157
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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158 ----------------------------------
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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159
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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160 Output file(s)
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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161 --------------
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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162
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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163 **Important** - the metric recorded output peak matrix/matrices is adjusted using the "The peak matrix should contain intensity | m/z | SNR values" parameter. By default, samples are presented row-wise and peak mass-to-charge ratio values are presented column-wise in each peak matrix, though this may be adjusted using the "Should rows or columns represent samples" parameter toggle.
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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164
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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165 @help_outputs_matrix@
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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166
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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167 ----------------------------------------------
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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168
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
computational-metabolomics
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169 @github_developers_contributors@
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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170 @license@
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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171 </help>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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172 <expand macro="citations" />
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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173 </tool>
5c545e1f0fa2 "planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"
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174