Mercurial > repos > galaxyp > proteomics_moff
annotate moff.xml @ 0:b4098353ee73 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
| author | galaxyp |
|---|---|
| date | Fri, 05 Jan 2018 12:47:36 -0500 |
| parents | |
| children | 8f0e76ad46ef |
| rev | line source |
|---|---|
|
0
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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1 <tool id="proteomics_moff" name="moFF" version="@VERSION@"> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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2 <description>extracts MS1 intensities from spectrum files</description> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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3 <macros> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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4 <token name="@VERSION@">1.2</token> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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5 <!-- xml macros, used for shared Galaxy parameter inputs --> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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6 <xml name="ident_input_macro" token_allow_multiple="true" token_input_type="data"> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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7 <!-- this is exactly the same across all three, except for allowing multiple in MBR and all but not in moff --> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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8 <conditional name="ident_input"> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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9 <param name="input_type_selector" type="select" label="Choose the format for the identification file:"> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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10 <option value="ps">Peptide Shaker PSM report (standard, not extended)</option> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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11 <option value="generic">Another tabular identification file</option> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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12 </param> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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13 <when value="ps"> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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14 <param name="ident_input_file" type="@INPUT_TYPE@" format="tabular" label="Peptide Shaker PSM report" multiple="@ALLOW_MULTIPLE@"/> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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15 </when> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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16 <when value="generic"> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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17 <param name="ident_input_file" type="@INPUT_TYPE@" format="tabular" label="A general tabular format" multiple="@ALLOW_MULTIPLE@" |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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18 help="Must have specific columns; see below to select these columns from your file. The file should have at most one header line. "/> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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19 <param name="remove_header" type="boolean" value="false" label="Remove the header line?" help="This is necessary if the file has a line with column headers"/> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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20 <param name="peptide" |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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21 type="data_column" |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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22 data_ref="ident_input_file" |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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23 label="Column with peptide-spectrum-match sequence"/> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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24 <param name="prot" |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
25 type="data_column" |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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26 data_ref="ident_input_file" |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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27 label="Column with protein ID"/> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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28 <param name="mod_peptide" |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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29 type="data_column" |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
30 data_ref="ident_input_file" |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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31 label="Column with peptide-spectrum-match sequence that contains possible modifications"/> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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32 <param name="rt" |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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33 type="data_column" |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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34 data_ref="ident_input_file" |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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35 label="Column with PSM retention time (in second)"/> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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36 <param name="mz" |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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37 type="data_column" |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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38 data_ref="ident_input_file" |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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39 label="Column with m/z (mass over charge)"/> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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40 <param name="mass" |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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41 type="data_column" |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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42 data_ref="ident_input_file" |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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43 label="Column with mass of the peptide"/> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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44 <param name="charge" |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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45 type="data_column" |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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46 data_ref="ident_input_file" |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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47 label="Column with charge of ionized peptide"/> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
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changeset
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48 </when> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
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49 </conditional> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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50 </xml> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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51 <xml name="raw_input_macro" token_allow_multiple="true" token_input_type="data"> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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52 <conditional name="msms_input"> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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53 <param name="input_type_selector" type="select" label="Choose the format for the MS/MS file"> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
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54 <option value="raw">Thermo RAW file</option> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
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55 <option value="mzml">mzML</option> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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56 </param> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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57 <when value="raw"> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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58 <param argument="--inputraw" type="@INPUT_TYPE@" multiple="@ALLOW_MULTIPLE@" format="raw" label="RAW file(s)"/> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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59 </when> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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60 <when value="mzml"> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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61 <param argument="--inputraw" type="@INPUT_TYPE@" multiple="@ALLOW_MULTIPLE@" format="mzml" label="mzML file(s)"/> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
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62 </when> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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63 </conditional> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
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64 </xml> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
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65 <!-- tokens (code snippets used in <command>) --> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
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66 <token name="@IDENT_INPUT_ARG_MULTIPLE@"><![CDATA[ |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
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67 ## this is where the ident input gets passed to moff/moff_all/moff_mbr |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
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68 --inputtsv |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
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69 #for $key in $task.ident_input.ident_input_file.keys(): |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
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70 './ident_inputs/${task.ident_input.ident_input_file[$key].display_name}' |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
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71 #end for |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
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72 ]]></token> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
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73 <token name="@IDENT_INPUT_ARG_SINGLE@"><![CDATA[ |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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74 ## this is where the ident input gets passed to moff/moff_all/moff_mbr |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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75 --inputtsv './ident_inputs/${task.ident_input.ident_input_file.display_name}' |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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76 ]]></token> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
77 <token name="@WRANGLE_IDENT_INPUT_SINGLE@"><![CDATA[ |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
78 mkdir ./ident_inputs && |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
79 #if $task.ident_input.input_type_selector == "ps": |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
80 ln -s '$task.ident_input.ident_input_file' './ident_inputs/$task.ident_input.ident_input_file.display_name' && |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
81 #else |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
82 ## optionally remove first line |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
83 #if $task.ident_input.remove_header: |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
84 sed -i '1d' '$task.ident_input.ident_input_file' && |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
85 #end if |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
86 ## header row with correct names: "peptide", "prot", "mod_peptide", "rt", "mz", "mass", and "charge" |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
87 echo -e "peptide\tprot\tmod_peptide\trt\tmz\tmass\tcharge" > tempfile.tab && |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
88 awk 'BEGIN{OFS="\t"; FS="\t"}{print \$pep,\$prot,\$mod,\$rt,\$mz,\$mass,\$charge}' pep="${task.ident_input.peptide}" prot="$task.ident_input.prot" mod="$task.ident_input.mod_peptide" rt="$task.ident_input.rt" mz="$task.ident_input.mz" mass="$task.ident_input.mass" charge="$task.ident_input.charge" '$task.ident_input.ident_input_file' >> tempfile.tab && |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
89 mv tempfile.tab '$task.ident_input.ident_input_file' && |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
90 ln -s '$task.ident_input.ident_input_file' './ident_inputs/$task.ident_input.ident_input_file.display_name' && |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
91 #end if |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
92 ]]></token> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
93 <token name="@WRANGLE_IDENT_INPUT_MULTIPLE@"><![CDATA[ |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
94 mkdir ./ident_inputs && |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
95 #if $task.ident_input.input_type_selector == "ps": |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
96 #for $key in $task.ident_input.ident_input_file.keys(): |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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97 ln -s '${task.ident_input.ident_input_file[$key]}' './ident_inputs/${task.ident_input.ident_input_file[$key].display_name}' && |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
98 #end for |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
99 #else |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
100 #for $key in $task.ident_input.ident_input_file.keys(): |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
101 ## optionally remove first line |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
102 #if $task.ident_input.remove_header: |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
103 sed -i '1d' '$task.ident_input.ident_input_file[$key]' && |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
104 #end if |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
105 ## header row with correct names: "peptide", "prot", "mod_peptide", "rt", "mz", "mass", and "charge" |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
106 echo -e "peptide\tprot\tmod_peptide\trt\tmz\tmass\tcharge" > tempfile.tab && |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
107 awk 'BEGIN{OFS="\t"; FS="\t"}{print \$pep,\$prot,\$mod,\$rt,\$mz,\$mass,\$charge}' pep="${task.ident_input.peptide}" prot="$task.ident_input.prot" mod="$task.ident_input.mod_peptide" rt="$task.ident_input.rt" mz="$task.ident_input.mz" mass="$task.ident_input.mass" charge="$task.ident_input.charge" '$filename' >> tempfile.tab && |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
108 mv tempfile.tab '$task.ident_input.ident_input_file[$key]' && |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
109 ln -s '$task.ident_input.ident_input_file[$key]' './ident_inputs/$task.ident_input.ident_input_file[$key].display_name' && |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
110 #end for |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
111 #end if |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
112 ]]></token> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
113 <token name="@RAW_INPUT_ARG_SINGLE@"><![CDATA[ |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
114 --inputraw './raws/$task.msms_input.inputraw.display_name' |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
115 ]]></token> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
116 <token name="@RAW_INPUT_ARG_MULTIPLE@"><![CDATA[ |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
117 --inputraw |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
118 #for $key in $task.msms_input.inputraw.keys(): |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
119 './raws/$task.msms_input.inputraw[$key].display_name' |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
120 #end for |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
121 ]]></token> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
122 <token name="@WRANGLE_RAW_INPUT_SINGLE@"><![CDATA[ |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
123 mkdir ./raws && |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
124 ## for files, need to softlink the display name to the history item |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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125 ln -s '$task.msms_input.inputraw' './raws/$task.msms_input.inputraw.display_name' && |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
126 ]]></token> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
127 <token name="@WRANGLE_RAW_INPUT_MULTIPLE@"><![CDATA[ |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
128 mkdir ./raws && |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
129 ## for files, need to softlink the display name to the history item |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
130 #for $key in $task.msms_input.inputraw.keys(): |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
131 ln -s '$task.msms_input.inputraw[$key]' './raws/$task.msms_input.inputraw[$key].display_name' && |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
132 #end for |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
133 ]]></token> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
134 </macros> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
135 <requirements> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
136 <requirement type="package" version="@VERSION@">moff</requirement> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
137 </requirements> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
138 <command detect_errors="aggressive"><![CDATA[ |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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139 mkdir ./out && |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
140 #if $task.task_selector == "moff": |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
141 @WRANGLE_IDENT_INPUT_SINGLE@ |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
142 @WRANGLE_RAW_INPUT_SINGLE@ |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
143 moff.py |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
144 @IDENT_INPUT_ARG_SINGLE@ |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
145 @RAW_INPUT_ARG_SINGLE@ |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
146 --tol $task.tol |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
147 --rt_w $task.rt_w |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
148 --rt_p $task.rt_p |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
149 --output_folder ./out |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
150 #if ($task.peptide_summary): |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
151 --peptide_summary 1 |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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152 #end if |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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parents:
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153 && |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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154 #if $task.peptide_summary: |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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155 mv ./out/peptide_summary_intensity_moFF_run.tab '$output_peptide_summary' && |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
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156 #end if |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
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157 mv ./out/*moff_result.txt '$output_table' |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
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158 && |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
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159 mv ./out/*.log '$output_logs' |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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160 #else if $task.task_selector == "mbr": |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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161 @WRANGLE_IDENT_INPUT_MULTIPLE@ |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
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162 moff_mbr.py |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
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163 --inputF ./ident_inputs |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
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164 --ext $task.ext |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
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165 && |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
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166 mv ./ident_inputs/mbr_output/* ./out |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
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167 #else: |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
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168 ## moff_all (mbr followed by apex) |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
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169 @WRANGLE_IDENT_INPUT_MULTIPLE@ |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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170 @WRANGLE_RAW_INPUT_MULTIPLE@ |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
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171 moff_all.py |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
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172 @IDENT_INPUT_ARG_MULTIPLE@ |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
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173 @RAW_INPUT_ARG_MULTIPLE@ |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
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174 --tol $task.tol |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
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175 --rt_w $task.rt_w |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
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176 --rt_p $task.rt_p |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
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177 --rt_p_match $task.rt_p_match |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
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178 --output_folder ./out |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
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179 --ext txt |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
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180 #if $task.peptide_summary: |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
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181 --peptide_summary 1 |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
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182 #end if |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
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183 && |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
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184 #if $task.peptide_summary: |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
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185 mv ./out/peptide_summary_intensity_moFF_run.tab '$output_peptide_summary' && |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
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186 #end if |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
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187 echo -ne |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
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188 #end if |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
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189 ]]></command> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
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|
190 <inputs> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
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191 <conditional name="task"> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
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192 <param name="task_selector" type="select" label="Choose which module to run"> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
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193 <option value="moff" selected="true">Apex intensity</option> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
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194 <option value="mbr">Match between runs</option> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
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195 <option value="all">All (match-between-runs followed by quantitation)</option> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
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196 </param> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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197 <when value = "moff"> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
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198 <expand macro="ident_input_macro" allow_multiple="false"/> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
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|
199 <expand macro="raw_input_macro" allow_multiple="false"/> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
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200 <param argument="--tol" type="float" value="10" label="Tolerance parameter" |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
201 help="Specify the tolerance parameter in ppm." /> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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202 <param argument="--rt_w" type="float" value="3.0" label="Retention time window" |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
203 help="Specify rt window for xic in minutes." /> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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204 <param argument="--rt_p" type="float" value="1" label="Time window for the peak" |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
205 help="Specify the time windows for the peak in minutes." /> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
206 <param argument="--rt_p_match" type="float" value="1.5" label="Time window for the matched peak" |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
207 help="Specify the time windows for the matched peak in minutes." /> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
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208 <param argument="--peptide_summary" type="boolean" value="true" label="Output the peptide summary?"/> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
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209 </when> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
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210 <when value="mbr"> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
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211 <expand macro="ident_input_macro" allow_multiple="false" input_type="data_collection"/> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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parents:
diff
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212 <param argument="--ext" type="text" value="tab" label="Provide the extension used in the display file name (without the period)"/> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
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213 </when> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
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214 <when value="all"> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
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215 <expand macro="ident_input_macro" allow_multiple="false" input_type="data_collection"/> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
216 <expand macro="raw_input_macro" allow_multiple="false" input_type="data_collection"/> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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217 <param argument="--tol" type="float" value="10" label="Tolerance parameter" |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
218 help="Specify the tolerance parameter in ppm." /> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
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219 <param argument="--rt_w" type="float" value="3.0" label="Retention time window" |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
220 help="Specify rt window for xic in minutes." /> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
221 <param argument="--rt_p" type="float" value="1" label="Time window for the peak" |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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222 help="Specify the time windows for the peak in minutes." /> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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223 <param argument="--rt_p_match" type="float" value="1.2" label="Time window for the matched peak" |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
224 help="Specify the time windows for the matched peak in minutes." /> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
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225 <param argument="--peptide_summary" type="boolean" value="true" label="Output the peptide summary?"/> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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226 </when> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
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227 </conditional> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
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228 </inputs> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
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229 <outputs> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
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230 <data format="tabular" name="output_table" label="${tool.name} quantification: ${on_string}"> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
231 <filter>task['task_selector']=='moff'</filter> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
232 </data> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
233 <data format="txt" name="output_logs" label="${tool.name} log: ${on_string}"> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
234 <filter>task['task_selector']=='moff'</filter> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
235 </data> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
236 <collection name="ident_output" type="list" label="${tool.name} quantification: ${on_string}"> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
237 <filter>task['task_selector']=='all' or task['task_selector']=='mbr'</filter> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
238 <!--discover datasets method --> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
239 <discover_datasets pattern="(?P<designation>.*)\.txt" directory="out" format="tabular"/> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
240 </collection> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
241 <collection name="log_output" type="list" label="${tool.name} logs: ${on_string}"> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
242 <filter>task['task_selector']=='all' or task['task_selector']=='mbr'</filter> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
243 <discover_datasets pattern="(?P<designation>.*)\.log" directory="out" format="txt"/> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
244 </collection> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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245 <data format="tabular" name="output_peptide_summary" label="${tool.name} peptide summary: ${on_string}"> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
246 <filter>task['peptide_summary']</filter> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
247 </data> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
248 </outputs> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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249 <tests> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
250 <!-- test moff_all --> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
251 <test> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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252 <param name="task_selector" value="all"/> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
253 <param name="input_type_selector" value="ps"/> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
254 <param name="ident_input_file"> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
255 <collection type="list"> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
256 <element name="mbr_test1" value="input/mbr_test1.tabular"/> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
257 <element name="mbr_test2" value="input/mbr_test2.tabular"/> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
258 </collection> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
259 </param> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
260 <param name="inputraw"> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
261 <collection type="list"> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
262 <element name="mbr_test1" value="input/mbr_test1.mzml"/> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
263 <element name="mbr_test2" value="input/mbr_test2.mzml"/> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
264 </collection> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
265 </param> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
266 <param name="peptide_summary" value="true"/> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
267 <output name="output_peptide_summary" ftype="tabular"> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
268 <assert_contents> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
269 <has_text text="sumIntensity_mbr_test1"/> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
270 <has_text text="sumIntensity_mbr_test2"/> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
271 </assert_contents> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
272 </output> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
273 <output_collection name="ident_output" type="list"> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
274 <element name="mbr_test1_match_moff_result" value="output1/mbr_test1_match_moff_result.txt"/> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
275 <element name="mbr_test2_match_moff_result" value="output1/mbr_test2_match_moff_result.txt"/> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
276 </output_collection> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
277 <output_collection name="log_output" type="list"> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
278 <element name="mbr_test1_match__moff"> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
279 <assert_contents> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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280 <has_line line="peptide at line 200 --> MZ: 783.4200 RT: 134.6997 matched (yes=1/no=0): 0"/> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
281 </assert_contents> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
282 </element> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
283 <element name="mbr_test2_match__moff"> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
284 <assert_contents> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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285 <has_line line="peptide at line 132 --> MZ: 767.8700 RT: 98.1975 matched (yes=1/no=0): 0"/> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
286 </assert_contents> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
287 </element> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
288 </output_collection> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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289 </test> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
290 <!-- test moff alone --> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
291 <test> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
292 <param name="task_selector" value="moff"/> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
293 <param name="input_type_selector" value="ps"/> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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294 <param name="ident_input_file" value="input/test.tabular" ftype="tabular"/> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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295 <param name="msms_input" value="mzml"/> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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296 <param name="inputraw" value="input/test.mzml" ftype="mzml"/> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
297 <param name="peptide_summary" value="true"/> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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298 <output name="output_peptide_summary" ftype="tabular" file="output2/moff_test_pepsum.tab"/> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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299 <output name="output_logs"> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
300 <assert_contents> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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301 <has_line line="peptide at line 294 --> MZ: 677.3300 RT: 60.6078"/> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
302 </assert_contents> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
303 </output> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
304 </test> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
305 <!-- test the generic input --> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
306 <test> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
307 <param name="task_selector" value="moff"/> |
|
b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
308 <param name="input_type_selector" value="generic"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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309 <param name="ident_input_file" value="input/test.tabular" ftype="tabular"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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310 <param name="remove_header" value="true"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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311 <param name="msms_input" value="mzml"/> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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312 <param name="inputraw" value="input/test.mzml" ftype="mzml"/> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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313 <param name="peptide" value="3"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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314 <param name="prot" value="2"/> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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315 <param name="mod_peptide" value="7"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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316 <param name="rt" value="13"/> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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317 <param name="mz" value="14"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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318 <param name="mass" value="17"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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319 <param name="charge" value="15"/> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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320 <param name="peptide_summary" value="true"/> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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321 <output name="output_peptide_summary" ftype="tabular" file="output2/moff_test_pepsum.tab"/> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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322 <output name="output_logs"> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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323 <assert_contents> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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324 <has_line line="peptide at line 294 --> MZ: 677.3300 RT: 60.6078"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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325 </assert_contents> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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326 </output> |
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327 </test> |
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328 <!-- test mbr --> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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329 <test> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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330 <param name="task_selector" value="mbr"/> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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331 <param name="input_type_selector" value="ps"/> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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332 <param name="ident_input_file"> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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333 <collection type="list"> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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334 <element name="mbr_test1" value="input/mbr_test1.tabular"/> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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335 <element name="mbr_test2" value="input/mbr_test2.tabular"/> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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336 </collection> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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337 </param> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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338 <param name="ext" value="tabular"/> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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339 <output_collection name="ident_output" type="list" count="2"> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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340 <element name="mbr_test1_match" file="input/mbr_output/mbr_test1_match.txt"/> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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341 <element name="mbr_test2_match" file="input/mbr_output/mbr_test2_match.txt"/> |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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342 </output_collection> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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343 </test> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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344 </tests> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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345 <help> |
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346 <![CDATA[ |
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347 **Description** |
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348 |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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349 moFF (a Modest Feature Finder) is an OS independent tool designed to extract |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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350 apex MS1 intensity using a set of identified MS2 peptides. |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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351 It currently uses a Go library to directly extract data from Thermo Raw spectrum files, |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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352 eliminating the need for conversions from other formats. |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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353 Moreover, moFF also allows one to work directly with mzML files. |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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354 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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355 **Usage** |
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356 |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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357 *Modules:* |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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358 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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359 1. Apex Intensity: this is used for a single pair of files, one identification and one spectrum file. |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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360 2. Match between runs (MBR): for multiple identification files, share MS2 identified peptides between runs and predict the retention time. |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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361 3. All (match between runs followed by apex intensity): this is used for more than one pair of identification and spectrum files. |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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362 |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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363 If both match between runs and apex intensity are desired, it is best to run them both at once (i.e., run the 'All' module). |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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364 The MBR module is mainly useful for observing the intermediate steps of the algorithm - its outputs are not able to be used as inputs in moFF or in other tools. |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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365 |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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366 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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367 *Inputs:* |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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368 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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369 - Identification file: this can either be a generic tabular file or the standard PSM report from PeptideShaker. |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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370 If it is a generic tabular file, please select the columns corresponding to the required information. |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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371 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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372 - MS/MS file: this can either be a Thermo raw file or an mzML file. |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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373 |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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374 A given pair of files must have the *exact* same display name, not including the extension; |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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375 e.g. ``example1.tabular`` and ``example1.mzml``. |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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376 If the display names are different, simply change them in the history menu. |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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377 |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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parents:
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378 For multiple files (the MBR or All modules), the identification and spectrum files must be provided as dataset collections. |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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379 This allows for usage of the output dataset collections in workflows. |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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parents:
diff
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380 |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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381 *Parameters:* |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
|
382 |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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parents:
diff
changeset
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383 All the parameters related to the the time windows (``rt_w``, ``rt_p``, ``rt_p_match``) are basically the |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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384 half of the entire time windows where the apex peak is searched or the XIC is retrieved. |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
galaxyp
parents:
diff
changeset
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385 For correct rt windows, we suggest you set the ``rt_p`` value equal to or slighly greater than the |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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386 dynamic exclusion duration set in your machine. We suggest also to set the |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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387 ``rt_p_match`` always slightly bigger than tha values used for ``rt_p``. |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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388 |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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389 *Outputs:* |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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390 |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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391 When used in the single file mode ("Apex intensity" module), the outputs are 2 (or 3) files: a log file, a quantitation file, |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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392 and (optionally) a peptide summary, with intensities aggregated across peptides. When used in the multiple file mode ("All"), |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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393 the outputs are a dataset collection of log files (one per identification file), a dataset collection of quantification files, and (optionally) a peptide summary. |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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394 |
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b4098353ee73
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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395 If used with a generic tabular format, the only columns in the output file are the 7 columns selected while using moFF plus the columns that moFF adds. Other columns are discarded. |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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396 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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397 **More Information** |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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398 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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399 See the moFF Github site at https://github.com/compomics/moFF, |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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400 and the publication at https://dx.doi.org/10.1038/nmeth.4075 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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401 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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402 ]]> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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403 </help> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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404 <citations> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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405 <citation type="doi">10.1038/nmeth.4075</citation> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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406 </citations> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94
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407 </tool> |