Mercurial > repos > galaxyp > pepquery
annotate pepquery.xml @ 3:962599ac5406 draft default tip
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit d23b1d8800e98af81496332ff7c051f8f25c73f6"
author | galaxyp |
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date | Wed, 12 Jan 2022 15:34:37 +0000 |
parents | 5b5a9f59e2c7 |
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rev | line source |
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2
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
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changeset
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1 <tool id="pepquery" name="PepQuery" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> |
0
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
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2 <description>Peptide-centric search engine for novel peptide identification and validation.</description> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
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3 <macros> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
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4 <import>macros.xml</import> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
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5 </macros> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
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changeset
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6 <requirements> |
2
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
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7 <requirement type="package" version="@TOOL_VERSION@">pepquery</requirement> |
0
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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8 </requirements> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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9 <stdio> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
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changeset
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10 <exit_code range="1:" level="fatal" description="Failed" /> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
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11 <regex match="Exception" |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
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12 source="stderr" |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
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13 level="fatal" |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
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14 description="java Exception" /> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
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15 </stdio> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
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16 <command><![CDATA[ |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
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17 #import re |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
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18 #set $spectrum_file = $re.sub('\s','_',$re.sub('[.][^.]*$','',$req_inputs.spectrum_file.display_name.split('/')[-1])) + ".mgf" |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
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19 #set $db_file = $re.sub('\s','_',$re.sub('[.][^.]*$','',$req_inputs.db_file.display_name.split('/')[-1])) + ".fa" |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
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20 ln -s '$req_inputs.spectrum_file' '$spectrum_file' && |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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21 ln -s '$req_inputs.db_file' '$db_file' && |
2
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
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22 #if $req_inputs.tags.tagType == 'pFind': |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
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23 pepquery main.java.util.generateTags '$req_inputs.tags.qry_res' > qry.tags && |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
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24 #end if |
0
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
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changeset
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25 pepquery |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
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changeset
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26 -ms '$spectrum_file' |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
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27 -db '$db_file' |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
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28 #if $req_inputs.input_type.input_type_selector == 'peptide' |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
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29 -pep '$req_inputs.input_type.multiple.input' |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
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30 #else |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
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31 -t '$req_inputs.input_type.input_type_selector' |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
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32 #if int(str($req_inputs.input_type.input_type_selector)) == 1 |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
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33 -i '$req_inputs.input_type.multiple.input' |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
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34 #else |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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35 -i '$req_inputs.input_type.input' |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
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36 #if int(str($req_inputs.input_type.input_type_selector)) == 2 |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
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37 #if $req_inputs.input_type.frame == 'None' |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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38 -f '0' |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
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39 #else |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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40 -f '$req_inputs.input_type.frame' |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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41 #end if |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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42 #else |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
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43 -anno '$req_inputs.input_type.anno' |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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44 #end if |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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45 #end if |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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46 #end if |
1
528bcf03e561
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 542fee4158c3dbd0c5ad8cd7e97b77f55982e0bf"
galaxyp
parents:
0
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47 -indexType $req_inputs.indexType |
2
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
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48 #if $req_inputs.tags.tagType == 'PepQuery': |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
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49 -tag '$req_inputs.tags.tag_file' |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
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50 -tagIndexType $req_inputs.tags.tagIndexType |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
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51 #elif $req_inputs.tags.tagType == 'pFind': |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
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52 -tag qry.tags |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
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53 -tagIndexType 2 |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
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54 #end if |
0
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
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55 #if $modifications.fixed_mod |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
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56 -fixMod '$modifications.fixed_mod' |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
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57 #end if |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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58 #if $modifications.var_mod |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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59 -varMod '$modifications.var_mod' |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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60 #end if |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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61 -maxVar '$modifications.max_mods' |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
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62 $modifications.unmodified |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
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63 $modifications.aa |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
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64 -tol '$ms_params.tolerance_params.precursor_tolerance' |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
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65 -tolu '$ms_params.tolerance_params.precursor_unit' |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
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66 -itol '$ms_params.tolerance_params.tolerance' |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
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67 -e '$ms_params.digestion.enzyme' |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
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68 -fragmentMethod '$ms_params.search.frag_method' |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
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69 -m '$ms_params.search.scoring_method' |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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70 -maxCharge '$ms_params.search.max_charge' |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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71 -minCharge '$ms_params.search.min_charge' |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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72 -minPeaks '$ms_params.search.min_peaks' |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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73 -minScore '$ms_params.search.min_score' |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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74 -maxLength '$ms_params.search.max_length' |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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75 -n '$ms_params.search.num_random_peptides' |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
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76 -o pepquery_output |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
77 | sed 's/No valid peptide/Error: No valid peptide/' | tee >(cat 1>&2) |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
78 #if $report_spectrum_file: |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
79 && for f in pepquery_output/psm.txt pepquery_output/psm_annotation.txt pepquery_output/detail.txt pepquery_output/psm_rank.txt; do if [ -e \${f} ]; then cp \${f} \${f}.orig; awk 'BEGIN{FS="\t"; OFS="\t"; stc = 0;}; NR==1{for (i = 1; i <= NF; i++) {if (\$i == "spectrum_title") stc = i;}}; NR==1{if (stc>0){\$stc = "spectrum_file" FS \$stc}; print}; NR>1{if (stc>0){\$stc = "$spectrum_file" FS \$stc}; print}' \${f}.orig > \${f};fi;done |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
80 #end if |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
81 ]]> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
82 </command> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
83 <inputs> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
84 <section name="req_inputs" title="Input Data" expanded="true"> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
85 <conditional name="input_type"> |
2
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
86 <param name="input_type_selector" argument="-t" type="select" label="Input Type" help="" > |
0
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
87 <option value="peptide">peptide</option> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
88 <option value="1">protein</option> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
89 <option value="2">DNA (translate to protein sequences)</option> |
2
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
90 <!-- these are not working with pepquery version 1.6 |
0
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
91 <option value="3">VCF (translate to protein sequences)</option> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
92 <option value="4">BED (translate to protein sequences)</option> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
93 <option value="5">GTF (translate to protein sequences)</option> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
94 --> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
95 </param> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
96 <when value="peptide"> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
97 <conditional name="multiple"> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
98 <param name="peptide_input_selector" type="select" label="Peptides?"> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
99 <option value="multiple">Peptide list from your history</option> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
100 <option value="single">Single peptide entered as text</option> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
101 </param> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
102 <when value="multiple"> |
2
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
103 <param name="input" argument="-pep" type="data" format="txt" label="Peptide Sequences (.txt)" help="Peptide sequence file containing peptides which you want to search (no column header, 1 peptide per line)." /> |
0
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
104 </when> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
105 <when value="single"> |
2
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
106 <param name="input" argument="-pep" type="text" label="Peptide Sequence" help="Peptide sequence which you want to search"> |
0
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
107 <validator type="regex" message="Must be AA letters">^[AC-IK-NP-TV-Yac-ik-np-tv-y]+$</validator> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
108 </param> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
109 </when> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
110 </conditional> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
111 </when> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
112 <when value="1"> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
113 <conditional name="multiple"> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
114 <param name="protein_input_selector" type="select" label="Proteins?"> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
115 <option value="multiple">Protein fasta from your history</option> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
116 <option value="single">Single protein entered as text</option> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
117 </param> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
118 <when value="multiple"> |
2
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
119 <param name="input" argument="-i" type="data" format="fasta" label="Protein Sequences (.txt)" help="Protein fasta file containing proteins which you want to search." /> |
0
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
120 </when> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
121 <when value="single"> |
2
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
122 <param name="input" argument="-i" type="text" label="Protein Sequence" help="Protein sequence which you want to search"> |
0
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
123 <validator type="regex" message="Must be AA letters">^[AC-IK-NP-TV-Yac-ik-np-tv-y]+$</validator> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
124 </param> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
125 </when> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
126 </conditional> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
127 </when> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
128 <when value="2"> |
2
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
129 <param name="input" argument="-i" type="text" label="DNA Sequence (at least 60 bp)" help="DNA sequence which you want to search"> |
0
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
130 <validator type="regex" message="Must be at least 60bp">^[acgtuAGCTU]{60}[acgtuAGCTU]*$</validator> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
131 </param> |
2
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
132 <param name="frame" argument="-f" type="select" label="Frame(s) for DNA translation" multiple="true" help="The frame(s) to translate DNA sequence to protein. Selecting nothing (default) keeps the longest frame"> |
0
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
133 <option value="1">1</option> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
134 <option value="2">2</option> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
135 <option value="3">3</option> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
136 <option value="4">4</option> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
137 <option value="5">5</option> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
138 <option value="6">6</option> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
139 </param> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
140 </when> |
2
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
141 <!-- these are not working with pepquery version 1.6 |
0
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
142 <when value="3"> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
143 <param name="input" type="data" format="vcf" label="VCF File" argument="-i" help="" /> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
144 <param name="anno" type="data_collection" label="Annotation Files" argument="-anno" help="Annotation files for the VCF file. Please follow preparation instructions here: http://bioconductor.org/packages/devel/bioc/html/PGA.html" /> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
145 </when> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
146 <when value="4"> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
147 <param name="input" type="data" format="bed" label="BED File" argument="-i" help="" /> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
148 <param name="anno" type="data_collection" label="Annotation Files" argument="-anno" help="Annotation files for the BED file. Please follow preparation instructions here: http://bioconductor.org/packages/devel/bioc/html/PGA.html" /> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
149 </when> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
150 <when value="5"> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
151 <param name="input" type="data" format="gtf" label="GTF File" argument="-i" help="" /> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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|
152 <param name="anno" type="data_collection" label="Annotation Files" argument="-anno" help="Annotation files for the GTF file. Please follow preparation instructions here: http://bioconductor.org/packages/devel/bioc/html/PGA.html" /> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
153 </when> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
154 --> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
155 </conditional> |
2
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
156 <param name="db_file" argument="-db" type="data" format="fasta" label="Protein Reference Database File" help="an input sequence that matches a reference will be ignored." /> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
157 <param name="spectrum_file" argument="-ms" type="data" format="mgf" label="Spectrum File" help="Spectrum file used for identification, mgf format" /> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
158 <param name="indexType" argument="-indexType" type="select" label="Report Spectrum Scan as" help="" > |
1
528bcf03e561
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 542fee4158c3dbd0c5ad8cd7e97b77f55982e0bf"
galaxyp
parents:
0
diff
changeset
|
159 <option value="1" selected="true">index (1-based) in MGF</option> |
528bcf03e561
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 542fee4158c3dbd0c5ad8cd7e97b77f55982e0bf"
galaxyp
parents:
0
diff
changeset
|
160 <option value="2">spectrum title in MGF</option> |
528bcf03e561
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 542fee4158c3dbd0c5ad8cd7e97b77f55982e0bf"
galaxyp
parents:
0
diff
changeset
|
161 </param> |
2
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
162 <conditional name="tags"> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
163 <param name="tagType" type="select" label="Tag File"> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
164 <option value="None">None</option> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
165 <option value="PepQuery">PepQuery</option> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
166 <option value="pFind">pFind</option> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
167 </param> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
168 <when value="None"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
169 <when value="PepQuery"> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
170 <param name="tag_file" argument="-tag" type="data" format="txt" label="PepPuery Tag File"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
171 <param name="tagIndexType" argument="-tagIndexType" type="select" label="Tag File Index Type" help="pFind uses the spectrum title" > |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
172 <option value="1">index (1-based) in MGF</option> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
173 <option value="2" selected="true">spectrum title in MGF</option> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
174 </param> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
175 </when> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
176 <when value="pFind"> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
177 <param name="qry_res" type="data" format="txt" label="pFind .qry.res" help="pFind can be used to generate a tags file for no-enzyme immunopeptidomics search" /> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
178 </when> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
179 </conditional> |
0
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
180 </section> |
2
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
181 |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
182 <!-- |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
183 <section name="tags" title="Tags File" expanded="false"> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
184 <param name="qry_res" type="data" format="txt" optional="true" label="pFind .qry.res" help="pFind can be used to generate a tags file for no-enzyme immunopeptidomics search" /> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
185 </section> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
186 --> |
0
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
187 <section name="modifications" title="Modifications" expanded="false"> |
2
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
188 <param name="fixed_mod" argument="-fixMod" type="select" label="Fixed modification(s)" multiple="true" help="Fixed modification"> |
0
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
189 <option value="6" selected="true">Carbamidomethylation of C (57.02146372057) modaa</option> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
190 <option value="117">Oxidation of M (15.99491461956) modaa</option> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
191 <expand macro="modifications" /> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
192 </param> |
2
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
193 <param name="var_mod" argument="-varMod" type="select" label="Variable modification(s)" multiple="true" help="Variable modification" > |
0
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
194 <option value="117" selected="true">Oxidation of M (15.99491461956) modaa</option> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
195 <option value="6">Carbamidomethylation of C (57.02146372057) modaa</option> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
196 <expand macro="modifications" /> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
197 </param> |
2
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
198 <param name="max_mods" argument="-maxVar" type="integer" label="Max Modifications" value="3" help="Max number of variable modifications" /> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
199 <param name="unmodified" argument="-um" type="boolean" truevalue="-um" falsevalue="" checked="false" label="Unmodified?" help="Validation with unrestricted modification searching" /> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
200 <param name="aa" argument="-aa" type="boolean" truevalue="-aa" falsevalue="" checked="false" label="Consider amino acid substitution modifications?" help="Whether or not to consider aa substitution modifications when perform modification filtering." /> |
0
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
201 </section> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
202 <section name="ms_params" title="Mass spectrometer" expanded="false"> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
203 <section name="tolerance_params" title="Tolerance" expanded="true"> |
2
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
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|
204 <param name="precursor_tolerance" argument="-tol" type="integer" value="10" label="Precursor Tolerance" help="the error window on experimental peptide mass values. This parameter is usually set according to the mass spectrometer which was used to generate the MS/MS data." /> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
205 <param name="precursor_unit" argument="-tolu" type="select" label="Precursor Unit" help="The unit of precursor ion m/z tolerance"> |
0
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
206 <option value="ppm" selected="true">ppm</option> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
207 <option value="Da">Da</option> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
208 </param> |
2
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
209 <param name="tolerance" argument="-itol" type="float" value="0.6" label="Tolerance" help="Error window for MS/MS fragment ion mass values in Da unit." /> |
0
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
210 </section> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
211 <section name="digestion" title="Digestion" expanded="false"> |
2
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
212 <param name="enzyme" argument="-e" type="select" label="Enzyme" help="Enzyme used for protein digestion" > |
0
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
213 <option value="0">Non enzyme</option> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
214 <option value="1" selected="true">Trypsin</option> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
215 <option value="2">Trypsin (no P rule)</option> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
216 <option value="3">Arg-C</option> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
217 <option value="4">Arg-C (no P rule)</option> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
218 <option value="5">Arg-N</option> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
219 <option value="6">Glu-C</option> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
220 <option value="7">Lys-C</option> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
221 </param> |
2
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
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|
222 <param name="max_missed_cleavages" argument="-c" type="integer" value="2" label="Max Missed Cleavages" help="The max missed cleavages" /> |
0
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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|
223 </section> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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|
224 <section name="search" title="PSM" expanded="false"> |
2
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
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|
225 <param name="frag_method" argument="-fragmentMethod" type="select" label="Fragmentation Method"> |
0
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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|
226 <option value="1" selected="true">CID/HCD</option> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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|
227 <option value="2">ETD</option> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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|
228 </param> |
2
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
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|
229 <param name="scoring_method" argument="-m" type="select" label="Scoring Method"> |
0
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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|
230 <option value="1" selected="true">HyperScore</option> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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|
231 <option value="2">MVH</option> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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|
232 </param> |
2
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
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|
233 <param name="max_charge" argument="-maxCharge" type="integer" value="3" label="Max Charge" help="The maximum charge to consider if the charge state is not available" /> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
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|
234 <param name="min_charge" argument="-minCharge" type="integer" value="2" label="Minimum Charge" help="The minimum charge to consider if the charge state is not available" /> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
235 <param name="min_peaks" argument="-minPeaks" type="integer" value="10" label="Minimum Peaks" help="Min peaks in spectrum" /> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
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|
236 <param name="min_score" argument="-minScore" type="integer" value="12" label="Minimum Score" help="Minimum score to consider for peptide searching" /> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
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|
237 <param name="max_length" argument="-maxLength" type="integer" value="45" label="Maximum length of peptide" help="The maximum length of peptide to consider." /> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
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|
238 <param name="num_random_peptides" argument="-n" type="integer" value="1000" label="Number of Random Peptides" help="The number of random peptides" /> |
0
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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|
239 </section> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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|
240 </section> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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|
241 <param name="report_spectrum_file" type="boolean" truevalue="spectrum_file," falsevalue="" checked="false" label="Add spectrum_file column" help="Add a spectrum_file column before the spectrum_title column. Useful for combining pepquery outputs." /> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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|
242 </inputs> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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|
243 <outputs> |
2
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
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|
244 <data name="query_tags" format="tabular" from_work_dir="qry.tags" label="${tool.name} on ${on_string}: tag file"> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
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|
245 <filter>req_inputs['tags']['tagType'] in ['pFind']</filter> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
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|
246 </data> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
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|
247 <data name="psm_annotation" format="tabular" from_work_dir="pepquery_output/psm_annotation.txt" label="${tool.name} on ${on_string}: PSM Annotation"> |
0
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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|
248 <actions> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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|
249 <action name="comment_lines" type="metadata" default="1" /> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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|
250 <action name="column_names" type="metadata" default="peptide,Query,calc_mr,observed_mz,charge,pepSeq,m_label,m_mz,m_intensity,mz,intensity" /> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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|
251 </actions> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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|
252 </data> |
2
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
253 <data name="detail" format="tabular" from_work_dir="pepquery_output/detail.txt" label="${tool.name} on ${on_string}: Detail"> |
0
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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|
254 <actions> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
255 <action name="comment_lines" type="metadata" default="1" /> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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|
256 <action name="column_names" type="metadata" default="${report_spectrum_file}spectrum_title,peptide,modification,pep_mass,score" /> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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|
257 </actions> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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|
258 </data> |
2
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
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|
259 <data name="psm" format="tabular" from_work_dir="pepquery_output/psm.txt" label="${tool.name} on ${on_string}: PSM"> |
0
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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|
260 <actions> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
261 <action name="comment_lines" type="metadata" default="1" /> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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|
262 <action name="column_names" type="metadata" default="peptide,modification,n,${report_spectrum_file}spectrum_title,charge,exp_mass,ppm,pep_mass,mz,score,n_db,total_db,n_random,total_random,pvalue" /> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
263 </actions> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
264 </data> |
2
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
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|
265 <data name="psm_rank_txt" format="tabular" from_work_dir="pepquery_output/psm_rank.txt" label="${tool.name} on ${on_string}: PSM Rank (txt)"> |
0
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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|
266 <actions> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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|
267 <action name="comment_lines" type="metadata" default="1" /> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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|
268 <action name="column_names" type="metadata" default="peptide,modification,n,${report_spectrum_file}spectrum_title,charge,exp_mass,ppm,pep_mass,mz,score,n_db,total_db,n_random,total_random,pvalue,rank,n_ptm" /> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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|
269 </actions> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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|
270 </data> |
2
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
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|
271 <data name="psm_rank_mgf" format="mgf" from_work_dir="pepquery_output/psm_rank.mgf" label="${tool.name} on ${on_string}: PSM Rank (mgf)"/> |
0
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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|
272 </outputs> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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|
273 <tests> |
2
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
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|
274 <!-- Test-1 --> |
0
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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|
275 <test> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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|
276 <section name="req_inputs"> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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|
277 <conditional name="input_type"> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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|
278 <param name="input_type_selector" value="peptide"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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|
279 <conditional name="multiple"> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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|
280 <param name="peptide_input_selector" value="single" /> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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|
281 <param name="input" value="ELGSSDLTAR"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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|
282 </conditional> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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|
283 </conditional> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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|
284 <param name="db_file" ftype="fasta" value="Uniprot.fasta"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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|
285 <param name="spectrum_file" ftype="mgf" value="iTRAQ_f4.mgf"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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|
286 </section> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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|
287 <section name="modifications"> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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|
288 <param name="fixed_mod" value="6,103,157"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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|
289 <param name="var_mod" value="117"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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|
290 <param name="max_mods" value="3"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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|
291 <param name="unmodified" value="False"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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|
292 <param name="aa" value="True"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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|
293 </section> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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|
294 <section name="ms_params"> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
295 <section name="tolerance_params"> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
296 <param name="precursor_tolerance" value="10"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
297 <param name="precursor_unit" value="ppm"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
298 <param name="tolerance" value="0.6"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
299 </section> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
300 <section name="digestion"> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
301 <param name="enzyme" value="0"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
302 <param name="max_missed_cleavages" value="2"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
303 </section> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
304 <section name="search"> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
305 <param name="frag_method" value="1"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
306 <param name="scoring_method" value="1"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
307 <param name="max_charge" value="3"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
308 <param name="min_charge" value="2"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
309 <param name="min_peaks" value="10"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
310 <param name="min_score" value="12"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
311 <param name="max_length" value="45"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
312 <param name="num_random_peptides" value="1000"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
313 </section> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
314 </section> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
315 <param name="report_spectrum_file" value="true"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
316 <output name="psm_rank_txt"> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
317 <assert_contents> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
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|
318 <has_text text="ELGSSDLTAR" /> |
2
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
319 <has_line_matching expression="ELGSSDLTAR\tiTRAQ 4-plex of peptide N-term@0\S+\t2\tiTRAQ_f4.mgf\t2\t2\t1191.6\d+\t2.0\d+\t1191.62\d+\t596.81\d+\t18.68\d+\t0\t20\t5\t995\t0.006\d+\t1"/> |
0
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
320 </assert_contents> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
321 </output> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
322 </test> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
323 |
2
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
324 <!-- Test-2 --> |
0
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
325 <test> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
326 <section name="req_inputs"> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
327 <conditional name="input_type"> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
328 <param name="input_type_selector" value="peptide"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
329 <conditional name="multiple"> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
330 <param name="peptide_input_selector" value="multiple" /> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
331 <param name="input" ftype="tabular" value="novel_peptides"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
332 </conditional> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
333 </conditional> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
334 <param name="db_file" ftype="fasta" value="Uniprot.fasta"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
335 <param name="spectrum_file" ftype="mgf" value="iTRAQ_f4.mgf"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
336 </section> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
337 <section name="modifications"> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
338 <param name="fixed_mod" value="6,103,157"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
339 <param name="var_mod" value="117"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
340 <param name="max_mods" value="3"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
341 <param name="unmodified" value="False"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
342 <param name="aa" value="True"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
343 </section> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
344 <section name="ms_params"> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
345 <section name="tolerance_params"> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
346 <param name="precursor_tolerance" value="10"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
347 <param name="precursor_unit" value="ppm"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
348 <param name="tolerance" value="0.6"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
349 </section> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
350 <section name="digestion"> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
351 <param name="enzyme" value="0"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
352 <param name="max_missed_cleavages" value="2"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
353 </section> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
354 <section name="search"> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
355 <param name="frag_method" value="1"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
356 <param name="scoring_method" value="1"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
357 <param name="max_charge" value="3"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
358 <param name="min_charge" value="2"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
359 <param name="min_peaks" value="10"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
360 <param name="min_score" value="12"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
361 <param name="max_length" value="45"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
362 <param name="num_random_peptides" value="1000"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
363 </section> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
364 </section> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
365 <param name="report_spectrum_file" value="true"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
366 <output name="psm_rank_txt"> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
367 <assert_contents> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
368 <has_text text="ELGSSDLTAR" /> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
369 <has_text text="SPYREFTDHLVK" /> |
2
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
370 <has_line_matching expression="SPYREFTDHLVK\tiTRAQ 4-plex of K@12\S+;iTRAQ 4-plex of peptide N-term@0\S+\t1\tiTRAQ_f4.mgf\t4\t3\t1778.\d+\t3.02\d+\t1778.95\d+\t593.99\d+\t12.17\d+\t2\t14\t-1\t-1\t100.0\t1"/> |
0
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
371 </assert_contents> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
372 </output> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
373 </test> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
374 |
2
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
375 <!-- Test-3 --> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
376 <test> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
377 <section name="req_inputs"> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
378 <conditional name="input_type"> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
379 <param name="input_type_selector" value="peptide"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
380 <conditional name="multiple"> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
381 <param name="peptide_input_selector" value="multiple" /> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
382 <param name="input" ftype="tabular" value="novel_peptides"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
383 </conditional> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
384 </conditional> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
385 <param name="db_file" ftype="fasta" value="Uniprot.fasta"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
386 <param name="spectrum_file" ftype="mgf" value="iTRAQ_f4.mgf"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
387 </section> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
388 <section name="modifications"> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
389 <param name="fixed_mod" value="6,103,157"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
390 <param name="var_mod" value="117"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
391 <param name="max_mods" value="3"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
392 <param name="unmodified" value="True"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
393 <param name="aa" value="True"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
394 </section> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
395 <section name="ms_params"> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
396 <section name="tolerance_params"> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
397 <param name="precursor_tolerance" value="10"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
398 <param name="precursor_unit" value="ppm"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
399 <param name="tolerance" value="0.6"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
400 </section> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
401 <section name="digestion"> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
402 <param name="enzyme" value="0"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
403 <param name="max_missed_cleavages" value="1"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
404 </section> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
405 <section name="search"> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
406 <param name="frag_method" value="1"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
407 <param name="scoring_method" value="1"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
408 <param name="max_charge" value="3"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
409 <param name="min_charge" value="2"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
410 <param name="min_peaks" value="7"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
411 <param name="min_score" value="10"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
412 <param name="max_length" value="45"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
413 <param name="num_random_peptides" value="1000"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
414 </section> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
415 </section> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
416 <param name="report_spectrum_file" value="false"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
417 <output name="psm_rank_txt"> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
418 <assert_contents> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
419 <has_text text="ELGSSDLTAR" /> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
420 <has_text text="SPYREFTDHLVK" /> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
421 <has_line_matching expression="ELGSSDLTAR\tiTRAQ 4-plex of peptide N-term@0\S+\t2\t3\t2\t1191.6\d+\t-3.04\d+\t1191.62\d+\t596.8\d+\t24.18\d+\t0\t22\t1\t995\t0.002\d+\t1\t0\tYes" /> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
422 </assert_contents> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
423 </output> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
424 </test> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
425 |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
426 <!-- Test-4 --> |
0
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
427 <test> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
428 <section name="req_inputs"> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
429 <conditional name="input_type"> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
430 <param name="input_type_selector" value="1"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
431 <conditional name="multiple"> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
432 <param name="protein_input_selector" value="multiple" /> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
433 <param name="input" ftype="fasta" value="novel_proteins.fa"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
434 </conditional> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
435 </conditional> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
436 <param name="db_file" ftype="fasta" value="Uniprot.fasta"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
437 <param name="spectrum_file" ftype="mgf" value="iTRAQ_f4.mgf"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
438 </section> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
439 <section name="modifications"> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
440 <param name="fixed_mod" value="6,103,157"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
441 <param name="var_mod" value="117"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
442 <param name="max_mods" value="3"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
443 <param name="unmodified" value="False"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
444 <param name="aa" value="True"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
445 </section> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
446 <section name="ms_params"> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
447 <section name="tolerance_params"> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
448 <param name="precursor_tolerance" value="10"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
449 <param name="precursor_unit" value="ppm"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
450 <param name="tolerance" value="0.6"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
451 </section> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
452 <section name="digestion"> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
453 <param name="enzyme" value="0"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
454 <param name="max_missed_cleavages" value="2"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
455 </section> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
456 <section name="search"> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
457 <param name="frag_method" value="1"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
458 <param name="scoring_method" value="1"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
459 <param name="max_charge" value="3"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
460 <param name="min_charge" value="2"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
461 <param name="min_peaks" value="10"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
462 <param name="min_score" value="12"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
463 <param name="max_length" value="45"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
464 <param name="num_random_peptides" value="1000"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
465 </section> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
466 </section> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
467 <param name="report_spectrum_file" value="true"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
468 <output name="psm_rank_txt"> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
469 <assert_contents> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
470 <has_text text="ELGSSDLTAR" /> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
471 <has_text text="SPYREFTDHLVK" /> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
472 </assert_contents> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
473 </output> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
474 </test> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
475 |
2
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
476 <!-- Test-5 --> |
0
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
477 <test> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
478 <section name="req_inputs"> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
479 <conditional name="input_type"> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
480 <param name="input_type_selector" value="2"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
481 <param name="input" value="gaactgggcagcagcgatctgaccgcgcgcagcccgtatcgcgaatttaccgatcatctggtgaaa"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
482 </conditional> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
483 <param name="db_file" ftype="fasta" value="Uniprot.fasta"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
484 <param name="spectrum_file" ftype="mgf" value="iTRAQ_f4.mgf"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
485 </section> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
486 <section name="modifications"> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
487 <param name="fixed_mod" value="6,103,157"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
488 <param name="var_mod" value="117"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
489 <param name="max_mods" value="3"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
490 <param name="unmodified" value="False"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
491 <param name="aa" value="True"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
492 </section> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
493 <section name="ms_params"> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
494 <section name="tolerance_params"> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
495 <param name="precursor_tolerance" value="10"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
496 <param name="precursor_unit" value="ppm"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
497 <param name="tolerance" value="0.6"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
498 </section> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
499 <section name="digestion"> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
500 <param name="enzyme" value="0"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
501 <param name="max_missed_cleavages" value="2"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
502 </section> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
503 <section name="search"> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
504 <param name="frag_method" value="1"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
505 <param name="scoring_method" value="1"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
506 <param name="max_charge" value="3"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
507 <param name="min_charge" value="2"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
508 <param name="min_peaks" value="10"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
509 <param name="min_score" value="12"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
510 <param name="max_length" value="45"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
511 <param name="num_random_peptides" value="1000"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
512 </section> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
513 </section> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
514 <param name="report_spectrum_file" value="true"/> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
515 <output name="psm_rank_txt"> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
516 <assert_contents> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
517 <has_text text="ELGSSDLTAR" /> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
518 </assert_contents> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
519 </output> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
520 </test> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
521 |
2
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
522 <!-- Test-6 --> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
523 <test> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
524 <section name="req_inputs"> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
525 <conditional name="input_type"> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
526 <param name="input_type_selector" value="peptide"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
527 <conditional name="multiple"> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
528 <param name="peptide_input_selector" value="multiple" /> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
529 <param name="input" ftype="tabular" value="novel_peptides"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
530 </conditional> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
531 </conditional> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
532 <param name="db_file" ftype="fasta" value="Uniprot.fasta"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
533 <param name="spectrum_file" ftype="mgf" value="immunopeptidomics.mgf"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
534 <param name="indexType" value="2"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
535 <conditional name="tags"> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
536 <param name="tagType" value="PepQuery"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
537 <param name="tag_file" ftype="tabular" value="test.tags"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
538 <param name="tagIndexType" value="2"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
539 </conditional> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
540 </section> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
541 <section name="modifications"> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
542 <param name="fixed_mod" value=""/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
543 <param name="var_mod" value="117,114,118,128"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
544 <param name="max_mods" value="3"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
545 <param name="unmodified" value="True"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
546 <param name="aa" value="True"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
547 </section> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
548 <section name="ms_params"> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
549 <section name="tolerance_params"> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
550 <param name="precursor_tolerance" value="20"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
551 <param name="precursor_unit" value="ppm"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
552 <param name="tolerance" value="0.02"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
553 </section> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
554 <section name="digestion"> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
555 <param name="enzyme" value="0"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
556 <param name="max_missed_cleavages" value="0"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
557 </section> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
558 <section name="search"> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
559 <param name="frag_method" value="1"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
560 <param name="scoring_method" value="1"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
561 <param name="max_charge" value="3"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
562 <param name="min_charge" value="2"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
563 <param name="min_peaks" value="10"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
564 <param name="min_score" value="12"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
565 <param name="max_length" value="25"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
566 <param name="num_random_peptides" value="1000"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
567 </section> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
568 </section> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
569 <param name="report_spectrum_file" value="true"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
570 <output name="psm_rank_txt"> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
571 <assert_contents> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
572 <has_text text="MTDRHAGTY" /> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
573 <has_text text="controllerType=0 controllerNumber=1 scan=19905" /> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
574 </assert_contents> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
575 </output> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
576 </test> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
577 |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
578 <!-- Test-7 --> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
579 <test> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
580 <section name="req_inputs"> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
581 <conditional name="input_type"> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
582 <param name="input_type_selector" value="peptide"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
583 <conditional name="multiple"> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
584 <param name="peptide_input_selector" value="multiple" /> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
585 <param name="input" ftype="tabular" value="novel_peptides"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
586 </conditional> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
587 </conditional> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
588 <param name="db_file" ftype="fasta" value="Uniprot.fasta"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
589 <param name="spectrum_file" ftype="mgf" value="immunopeptidomics.mgf"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
590 <param name="indexType" value="2"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
591 <conditional name="tags"> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
592 <param name="tagType" value="pFind"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
593 <param name="qry_res" ftype="txt" value="pFind.qry.res"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
594 </conditional> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
595 </section> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
596 <section name="modifications"> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
597 <param name="fixed_mod" value=""/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
598 <param name="var_mod" value="117,114,118,128"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
599 <param name="max_mods" value="3"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
600 <param name="unmodified" value="True"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
601 <param name="aa" value="True"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
602 </section> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
603 <section name="ms_params"> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
604 <section name="tolerance_params"> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
605 <param name="precursor_tolerance" value="20"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
606 <param name="precursor_unit" value="ppm"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
607 <param name="tolerance" value="0.02"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
608 </section> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
609 <section name="digestion"> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
610 <param name="enzyme" value="0"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
611 <param name="max_missed_cleavages" value="0"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
612 </section> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
613 <section name="search"> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
614 <param name="frag_method" value="1"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
615 <param name="scoring_method" value="1"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
616 <param name="max_charge" value="3"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
617 <param name="min_charge" value="2"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
618 <param name="min_peaks" value="10"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
619 <param name="min_score" value="12"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
620 <param name="max_length" value="25"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
621 <param name="num_random_peptides" value="1000"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
622 </section> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
623 </section> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
624 <param name="report_spectrum_file" value="true"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
625 <output name="psm_rank_txt"> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
626 <assert_contents> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
627 <has_text text="MTDRHAGTY" /> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
628 <has_text text="controllerType=0 controllerNumber=1 scan=19905" /> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
629 </assert_contents> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
630 </output> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
631 <output name="query_tags" file="test.tags"/> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
632 <!-- |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
633 --> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
634 </test> |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
635 |
0
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
636 </tests> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
637 <help><![CDATA[ |
2
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
638 **PepQuery** |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
639 |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
640 PepQuery_ is a peptide-centric search engine for novel peptide identification and validation. Cancer genomics studies have identified a large number of genomic alterations that may lead to novel, cancer-specific protein sequences. Proteins resulted from these genomic alterations are attractive candidates for cancer biomarkers and therapeutic targets. The leading approach to proteomic validation of genomic alterations is to analyze tandem mass spectrometry (MS/MS) data using customized proteomics databases created from genomics data. Such analysis is time-consuming and requires thorough training and detailed knowledge in proteomics data analysis, leading to a gap between MS/MS data and the cancer genomics community. PepQuery does not require customized databases and allows quick and easy proteomic validation of genomic alterations. |
0
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
641 |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
642 **Inputs** |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
643 - A sequence to match, one of the following: |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
644 |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
645 - A peptide string or a history dataset with a list of peptides |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
646 - A protein string or a history dataset with a protein fasta |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
647 - A DNA string that is at least 60 base pairs in length |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
648 |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
649 - A mass spectrometry MGF file |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
650 - A reference protein fasta database, peptides matching a reference sequence will be excluded. |
2
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
651 - An optional tags file for no-enzyme immunopeptidomics search |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
652 |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
653 - See: http://pepquery.org/data/PepQuery_for_immunopeptidomics_data.pdf |
0
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
654 |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
655 **Outputs** |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
656 - PSM annotation - tabular with columns: |
2
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
657 |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
658 - peptide Query calc_mr observed_mz charge pepSeq m_label m_mz m_intensity mz intensity |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
659 |
0
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
660 - Detail - tabular with columns: |
2
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
661 |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
662 - *report_spectrum_file* spectrum_title peptide modification pep_mass score |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
663 |
0
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
664 - PSM - tabular with columns: |
2
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
665 |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
666 - peptide modification n *report_spectrum_file* spectrum_title charge exp_mass ppm pep_mass mz score n_db total_db n_random total_random pvalue |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
667 |
0
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
668 - PSM Rank - tabular with columns: |
2
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
669 |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
670 - peptide modification n *report_spectrum_file* spectrum_title charge exp_mass ppm pep_mass mz score n_db total_db n_random total_random pvalue rank *n_ptm* |
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
671 |
0
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
672 - An MGF with the best matching spectrums |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
673 |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
parents:
diff
changeset
|
674 The *report_spectrum_file* is an optional field that can be added. |
2
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
galaxyp
parents:
1
diff
changeset
|
675 |
0
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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676 The *n_ptm* field is added when using unrestricted modification searching (-um). |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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677 |
2
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
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678 .. _PepQuery: http://pepquery.org/document.html |
0
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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679 |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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680 ]]></help> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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681 <citations> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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682 <citation type="doi">10.1101/gr.235028.118</citation> |
2
5b5a9f59e2c7
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 8b553bb3e585b03c670a3689d4fe6eef7e464407"
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683 <citation type="doi">10.1038/s41467-020-15456-w</citation> |
0
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
galaxyp
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684 </citations> |
32d3818fc635
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery commit 9764eee2801a65462d26b919bfaea6e3ae0cce7a"
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685 </tool> |