Mercurial > repos > galaxyp > mz_to_sqlite
annotate mz_to_sqlite.xml @ 1:e34bdac5b157 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit abf01d5c1b700697fc9d86ef2666349f99bae93e
author | galaxyp |
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date | Wed, 28 Mar 2018 09:33:18 -0400 |
parents | ab33bd49de43 |
children | 1320693cbf1e |
rev | line source |
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1
e34bdac5b157
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit abf01d5c1b700697fc9d86ef2666349f99bae93e
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1 <tool id="mz_to_sqlite" name="mz to sqlite" version="2.0.0"> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit 078c2920db4203a2b7525fd819716507e9346546-dirty
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2 <description>Extract mzIdentML and associated proteomics datasets into a SQLite DB</description> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit 078c2920db4203a2b7525fd819716507e9346546-dirty
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3 <requirements> |
1
e34bdac5b157
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit abf01d5c1b700697fc9d86ef2666349f99bae93e
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4 <requirement type="package" version="2.0.0">mztosqlite</requirement> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit 078c2920db4203a2b7525fd819716507e9346546-dirty
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5 </requirements> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit 078c2920db4203a2b7525fd819716507e9346546-dirty
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6 <stdio> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit 078c2920db4203a2b7525fd819716507e9346546-dirty
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7 <exit_code range="1:" level="fatal" description="Error Running mz_to_sqlite" /> |
ab33bd49de43
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit 078c2920db4203a2b7525fd819716507e9346546-dirty
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8 </stdio> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit 078c2920db4203a2b7525fd819716507e9346546-dirty
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9 <command> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit 078c2920db4203a2b7525fd819716507e9346546-dirty
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10 <![CDATA[ |
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e34bdac5b157
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit abf01d5c1b700697fc9d86ef2666349f99bae93e
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11 mz_to_sqlite -Xms1g -Xmx6g |
e34bdac5b157
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit abf01d5c1b700697fc9d86ef2666349f99bae93e
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12 -numthreads "\${GALAXY_SLOTS:-4}" |
e34bdac5b157
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit abf01d5c1b700697fc9d86ef2666349f99bae93e
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13 -dbname 'sqlite.db' |
e34bdac5b157
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit abf01d5c1b700697fc9d86ef2666349f99bae93e
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14 -mzid '$mzinput' |
e34bdac5b157
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit abf01d5c1b700697fc9d86ef2666349f99bae93e
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15 #if len($scanfiles) > 0: |
e34bdac5b157
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit abf01d5c1b700697fc9d86ef2666349f99bae93e
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16 #set $files = " ".join(["'"+ a.strip() + "'" for a in str($scanfiles).split(',')]) |
e34bdac5b157
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit abf01d5c1b700697fc9d86ef2666349f99bae93e
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17 -scanfiles $files |
e34bdac5b157
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit abf01d5c1b700697fc9d86ef2666349f99bae93e
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18 #set $dfiles = [a for a in $scanfiles] |
e34bdac5b157
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit abf01d5c1b700697fc9d86ef2666349f99bae93e
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19 -scanFilesDisplayName |
e34bdac5b157
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit abf01d5c1b700697fc9d86ef2666349f99bae93e
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20 #for $f in $dfiles |
e34bdac5b157
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit abf01d5c1b700697fc9d86ef2666349f99bae93e
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21 '$f.display_name' |
e34bdac5b157
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit abf01d5c1b700697fc9d86ef2666349f99bae93e
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22 #end for |
e34bdac5b157
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit abf01d5c1b700697fc9d86ef2666349f99bae93e
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23 #end if |
e34bdac5b157
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit abf01d5c1b700697fc9d86ef2666349f99bae93e
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24 #if len($searchdbs) > 0: |
e34bdac5b157
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit abf01d5c1b700697fc9d86ef2666349f99bae93e
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25 #set $dbFiles = " ".join(["'"+ a.strip() + "'" for a in str($searchdbs).split(',')]) |
e34bdac5b157
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit abf01d5c1b700697fc9d86ef2666349f99bae93e
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26 -fasta $dbFiles |
e34bdac5b157
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit abf01d5c1b700697fc9d86ef2666349f99bae93e
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27 #end if |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit 078c2920db4203a2b7525fd819716507e9346546-dirty
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28 ]]> |
ab33bd49de43
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit 078c2920db4203a2b7525fd819716507e9346546-dirty
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29 </command> |
ab33bd49de43
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit 078c2920db4203a2b7525fd819716507e9346546-dirty
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30 <inputs> |
1
e34bdac5b157
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit abf01d5c1b700697fc9d86ef2666349f99bae93e
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31 <param name="mzinput" type="data" format="mzid" label="Proteomics Identification files"/> |
0
ab33bd49de43
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit 078c2920db4203a2b7525fd819716507e9346546-dirty
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32 <param name="scanfiles" type="data" format="mzml,mgf" multiple="true" optional="true" label="Proteomics Spectrum files"/> |
ab33bd49de43
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit 078c2920db4203a2b7525fd819716507e9346546-dirty
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33 <param name="searchdbs" type="data" format="fasta,uniprotxml" multiple="true" optional="true" label="Proteomics Search Database Fasta" |
ab33bd49de43
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit 078c2920db4203a2b7525fd819716507e9346546-dirty
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34 help="These can provide sequences and length for proteins if not already present in the mzIdentML input"/> |
ab33bd49de43
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit 078c2920db4203a2b7525fd819716507e9346546-dirty
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35 </inputs> |
ab33bd49de43
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit 078c2920db4203a2b7525fd819716507e9346546-dirty
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36 <outputs> |
1
e34bdac5b157
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit abf01d5c1b700697fc9d86ef2666349f99bae93e
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37 <data format="mz.sqlite" name="sqlite_db" label="${tool.name} on ${on_string}" from_work_dir="sqlite.db"/> |
0
ab33bd49de43
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit 078c2920db4203a2b7525fd819716507e9346546-dirty
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38 </outputs> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit 078c2920db4203a2b7525fd819716507e9346546-dirty
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39 <tests> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit 078c2920db4203a2b7525fd819716507e9346546-dirty
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40 <test> |
ab33bd49de43
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit 078c2920db4203a2b7525fd819716507e9346546-dirty
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41 </test> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit 078c2920db4203a2b7525fd819716507e9346546-dirty
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42 </tests> |
ab33bd49de43
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit 078c2920db4203a2b7525fd819716507e9346546-dirty
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43 <help> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit 078c2920db4203a2b7525fd819716507e9346546-dirty
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44 <![CDATA[ |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit 078c2920db4203a2b7525fd819716507e9346546-dirty
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45 ** mz_to_sqlite converts proteomics file formats to a SQLite database** |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit 078c2920db4203a2b7525fd819716507e9346546-dirty
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46 |
ab33bd49de43
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit 078c2920db4203a2b7525fd819716507e9346546-dirty
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47 ]]> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit 078c2920db4203a2b7525fd819716507e9346546-dirty
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48 </help> |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite commit 078c2920db4203a2b7525fd819716507e9346546-dirty
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49 </tool> |