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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
author galaxyp
date Mon, 21 Jun 2021 12:50:54 +0000
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3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
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1 <tool id="diffacto" name="Diffacto" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5">
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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2 <description>Comparative Protein Abundance from Covariation of Peptide Abundances</description>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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3 <macros>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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4 <token name="@TOOL_VERSION@">1.0.6</token>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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5 <token name="@VERSION_SUFFIX@">0</token>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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6 </macros>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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7 <requirements>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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8 <requirement type="package" version="@TOOL_VERSION@">diffacto</requirement>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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9 </requirements>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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10 <command detect_errors="exit_code"><![CDATA[
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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11 tr '\t' ',' < '$input' > input.csv &&
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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12 diffacto
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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13 -i input.csv
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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14 #if $db
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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15 -db '$db'
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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16 #end if
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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17 #if $samples
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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18 -samples '$samples'
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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19 #end if
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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20 -reference '$reference'
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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21 #if $normalize
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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22 -normalize $normalize
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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23 #end if
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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24 #if $farms_mu
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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25 -farms_mu $farms_mu
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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26 #end if
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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27 #if $farms_alpha
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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28 -farms_alpha $farms_alpha
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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29 #end if
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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30 -min_samples $min_samples
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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31 -impute_threshold $impute_threshold
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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32 -cutoff_weight $cutoff_weight
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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33 $use_unique
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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34 #if $scale == 'log2'
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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35 -log2 True
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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36 #else
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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37 -log2 False
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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38 #end if
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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39 $fast
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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40 -out '$output'
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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41 #if $mcfdr
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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42 -mc_out '$mc_out'
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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43 #end if
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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44 #if $loadings
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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45 -loadings_out '$loadings_out'
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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46 #end if
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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47 ]]></command>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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48 <inputs>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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49 <param name="input" argument="-i" type="data" format="tabular,csv" label="Peptides abundances">
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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50 <help><![CDATA[
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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51 Peptides abundances in tabular or csv format.
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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52 <ul>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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53 <li>The first row is column headers and should contain the sample name for each sample column. </li>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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54 <li>The first column should contain unique peptide sequences. </li>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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55 <li><i>Optionally, the second column may be ProteinID assignments, else the <b>Protein database</b> input is required.</i></li>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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56 <li>Each remaining column is a sample column with numeric abundance values.</li>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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57 <li>Missing values should be empty instead of zeros.</li>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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58 </ul>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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59 ]]></help>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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60 </param>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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61 <param argument="-db" type="data" format="fasta" label="Protein database" optional="true"
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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62 help="Required if the Peptide abundances input does not have Protein IDs in the second column"/>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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63 <param argument="-samples" type="data" format="tabular" label="Sample Groups" optional="true">
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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64 <help><![CDATA[
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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65 <i>Optional: By default, each Sample column in Peptide abundances is treated as a singleton group.</i>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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66 <br>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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67 Groups the samples from the Peptides abundance input for comparison.
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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68 Each sample column from Peptides abundance input should be on a line with 2 columns:
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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69 <ol>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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70 <li>Sample name for header line of the Peptides abundance input.</li>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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71 <li>Group Name assignemnt for the sample</li>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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72 </ol>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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73 ]]></help>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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74 </param>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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75 <param argument="-reference" type="text" value="" label="Reference sample groups" optional="true">
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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76 <help><![CDATA[
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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77 <i>Optional: By default, Diffacto uses the average of all samples/groups as the reference.</i>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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78 <br>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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79 Names of sample groups <i>(separated by semicolon)</i> treated as the comparison reference.
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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80 <ul>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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81 <li>If a Sample Groups input was used, the reference names should be Group names from column 2.</li>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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82 <li>Otherwise, the reference names should be Sample names from the Peptides abundance column header line.</li>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
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83 </ul>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
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84 ]]></help>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
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85 </param>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
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86 <param name="scale" argument="-log2" type="select" label="Peptides abundance scale">
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
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87 <option value="linear">linear</option>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
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88 <option value="log2">log2</option>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
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89 </param>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
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90 <param argument="-normalize" type="select" label="Sample-wise normalization" optional="true">
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
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91 <option value="average">average</option>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
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92 <option value="median">median</option>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
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93 <option value="GMM">GMM</option>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
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94 </param>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
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95 <param argument="-farms_mu" type="float" value="0.1" min="0.0" max="1.0" optional="true" label="Hyperparameter mu"
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
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96 help="Hyperparameter mu (default: 0.1)"/>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
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97 <param argument="-farms_alpha" type="float" value="0.1" min="0.0" max="1.0" optional="true" label="Hyperparameter alpha"
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
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98 help="Hyperparameter weight of prior probability (default: 0.1)"/>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
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99 <param argument="-min_samples" type="integer" value="1" min="1" label="Minimum samples for peptide"
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
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100 help="Minimum number of samples peptides needed to be quantified in"/>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
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101 <param argument="-impute_threshold" type="float" value="0.99" min="0.1" max="1.0" label="Minimum fraction of missing values in the group"
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
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102 help="Impute missing values if missing fraction is larger than the threshold."/>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
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103 <param argument="-cutoff_weight" type="float" value="0.5" min="0." max="1.0" label="Peptide cutoff weight"
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
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104 help="Peptides weighted lower than the cutoff will be excluded."/>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
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105 <param argument="-use_unique" type="boolean" truevalue="-use_unique True" falsevalue="" checked="false" label="Use unique peptides only"/>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
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106 <param argument="-fast" type="boolean" truevalue="-fast True" falsevalue="" checked="false" label="Allow early termination in EM calculation when noise is sufficiently small."/>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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107 <param name="mcfdr" argument="-mc_out" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Perform Monte Carlo FDR simulation"/>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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108 <param name="loadings" argument="-loadings_out" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Output Protein Peptide loadings file"/>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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109 </inputs>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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110 <outputs>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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111 <data name="output" format="tabular" label="${tool.name} on ${on_string}: Protein Abundance">
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
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112 <actions>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
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113 <action name="comment_lines" type="metadata" default="1" />
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
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114 <action name="column_names" type="metadata" default="Protein,N.Pept,Q.Pept,S/N,P(PECA)" />
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
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115 </actions>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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116 </data>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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117 <data name="mc_out" format="tabular" label="${tool.name} on ${on_string}: MC FDR">
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
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118 <filter>mcfdr == True</filter>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
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119 <actions>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
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120 <action name="comment_lines" type="metadata" default="1" />
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
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121 <action name="column_names" type="metadata" default="Protein,P(MC),MCFDR" />
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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122 </actions>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
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123 </data>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
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124 <data name="loadings_out" format="tabular" label="${tool.name} on ${on_string}: Protein Peptide loading">
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
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125 <filter>loadings == True</filter>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
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126 <actions>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
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127 <action name="comment_lines" type="metadata" default="1" />
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
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128 <action name="column_names" type="metadata" default="Protein,Peptide,Loading" />
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
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129 </actions>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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130 </data>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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131 </outputs>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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132 <tests>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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133 <test>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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134 <param name="input" ftype="csv" value="HBY20Mix.peptides.csv"/>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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135 <param name="db" ftype="fasta" value="UP000002311_559292.fasta"/>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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136 <param name="samples" ftype="tabular" value="HBY20Mix.samples.lst"/>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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137 <output name="output">
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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138 <assert_contents>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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139 <has_text text="P19097" />
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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140 </assert_contents>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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141 </output>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
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142 </test>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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143 <test>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
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144 <param name="input" ftype="tabular" value="HBY20Mix.peptides.tsv"/>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
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145 <param name="db" ftype="fasta" value="UP000002311_559292.fasta"/>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
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146 <param name="samples" ftype="tabular" value="HBY20Mix.samples.lst"/>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
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147 <output name="output">
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
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148 <assert_contents>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
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149 <has_text text="P19097" />
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
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150 </assert_contents>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
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151 </output>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
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152 </test>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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153
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
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154 <test>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
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155 <param name="input" ftype="csv" value="iPRG.novo.pep.csv"/>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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156 <param name="samples" ftype="tabular" value="iPRG.samples.lst"/>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
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157 <param name="min_samples" value="2"/>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
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158 <output name="output">
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
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159 <assert_contents>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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160 <has_text text="FAS2" />
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
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161 </assert_contents>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
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162 </output>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
163 </test>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
164 <test>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
165 <param name="input" ftype="csv" value="iPRG.novo.pep.csv"/>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
166 <param name="samples" ftype="tabular" value="iPRG.samples.lst"/>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
167 <param name="min_samples" value="4"/>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
168 <param name="use_unique" value="True"/>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
169 <param name="mcfdr" value="True"/>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
170 <output name="output">
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
171 <assert_contents>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
172 <has_text text="FAS2" />
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
173 </assert_contents>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
174 </output>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
175 <output name="mc_out">
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
176 <assert_contents>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
177 <has_text text="FAS2" />
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
178 </assert_contents>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
179 </output>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
180 </test>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
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181
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
182 </tests>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
183 <help><![CDATA[
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
184 **Diffacto**
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
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diff changeset
185
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
186 Diffacto_ quantifies comparative protein abundance from the covariation of peptide abundances.
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
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diff changeset
187
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
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diff changeset
188 Diffacto_ applies factor analysis to extract the covariation of peptides' abundances. The method enables a weighted geometrical average summarization and automatic elimination of incoherent peptides, which may result from suboptimal digestion or being partially modified, and are not representative of the protein concentration.
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
189
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
190 **Inputs**
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
191
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
192 - **Peptides abundances** *in tabular or csv format*
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
193
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
194 - The first row is column headers and should contain the sample name for each sample column.
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
195 - The first column should contain unique peptide sequences.
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
196 - *Optionally, the second column may be Protein ID assignments, else the* **Protein database** *input is required.*
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
197 - Each remaining column is a sample column with numeric abundance values.
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
198 - Missing values should be empty instead of zeros.
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
199 - Example:
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
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200
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
201 ============ ========== ========= ========= ========= =========
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
202 sequences Protein Sample1-A Sample1_B Sample2_A Sample2_B
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
203 ============ ========== ========= ========= ========= =========
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
204 AAATAAMTK EF3A 127.35209 142.58217 135.89206 162.54500
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
205 AAATTGEWDK PDC1 100.35922 114.68676 922.60617 833.97955
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
206 LPVLLADACCSR HSP72;PDC1 120.21570 194.99594 977.48321 219.23281
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
207 AAEEAGVTDVK FAS2 442.67501 457.52266 448.52837 424.15980
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
208 ============ ========== ========= ========= ========= =========
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
209
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
210
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
211 - **Protein database** *(optional)*
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
212
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
213 - The Protein database in fasta format that has protein seqeunces containing the peptides.
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
214 - Required if the **Peptides abundances** input does not have a second column containing Protein ID assignments
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
215
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
216
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
217 - **Sample Groups** *(optional)*
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
218
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
219 - First column has the sample name
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
220 - Second column has the group name
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
221 - Example:
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
222
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
223 ========= ==
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
224 Sample1-A S1
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
225 Sample1_B S1
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
226 Sample2_A S2
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
227 Sample2_B S2
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
228 ========= ==
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
229
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
230
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
231 **Outputs**
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
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diff changeset
232
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
233 - **Protein Abundance**
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
234
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
235 ======= ====== ====== =================== =================== ================== ==================
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
236 Protein N.Pept Q.Pept S/N P(PECA) S1 S2
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
237 ======= ====== ====== =================== =================== ================== ==================
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
238 EF3A 2 2 -2.874362404756714 0.2608189432601452 463172795.59269696 489796576.81520355
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
239 FAS2 6 4 -0.5901265476375578 0.8395809777778386 52093246.23323742 53280470.3811749
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
240 PDC1 3 2 6.634988423694361 0.25491030879514676 203769831.79809052 174641994.14231393
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
241 ======= ====== ====== =================== =================== ================== ==================
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
242
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
243 - **FDR Estimate from Monte Carlo Simulation** *(optional)*
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
244
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
galaxyp
parents:
diff changeset
245 ======= =================== ===================
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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246 Protein P(MC) MCFDR
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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247 ======= =================== ===================
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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248 EF3A 0.1419053964023984 0.5287482885321804
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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249 FAS2 0.9867109634551495 0.9132662960822688
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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250 PDC1 0.3338088445078459 0.5287482885321804
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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251 ======= =================== ===================
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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252
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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253 - **Protein Peptide Loadings** *(optional)*
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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254
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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255 ======= =========== ===================
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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256 EF3A AAATAAMTK 0.5287482885321804
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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257 FAS2 AAEEAGVTDVK 0.9132662960822688
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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258 PDC1 AAATTGEWDK 0.5287482885321804
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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259 ======= =========== ===================
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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260
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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261 .. _Diffacto: https://github.com/statisticalbiotechnology/diffacto
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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262
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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263 ]]></help>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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264 <citations>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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265 <citation type="doi">10.1074/mcp.O117.067728</citation>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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266 </citations>
3cc7ce0822a1 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto commit 507bb20a2c246bb0a1a0c7dae1555a851730e4a6"
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267 </tool>