Mercurial > repos > bgruening > diamond
annotate macros.xml @ 6:64be1ac21109 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
author | bgruening |
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date | Thu, 27 Sep 2018 06:30:30 -0400 |
parents | df7738595640 |
children | 62c9df8382c2 |
rev | line source |
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df7738595640
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents:
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changeset
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1 <macros> |
6
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
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2 <token name="@VERSION@">0.9.21</token> |
1
df7738595640
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents:
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changeset
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3 |
df7738595640
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents:
diff
changeset
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4 <xml name="requirements"> |
df7738595640
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents:
diff
changeset
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5 <requirements> |
df7738595640
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents:
diff
changeset
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6 <requirement type="package" version="@VERSION@">diamond</requirement> |
df7738595640
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents:
diff
changeset
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7 </requirements> |
df7738595640
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents:
diff
changeset
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8 </xml> |
df7738595640
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents:
diff
changeset
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9 |
df7738595640
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents:
diff
changeset
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10 <xml name="stdio"> |
df7738595640
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents:
diff
changeset
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11 <stdio> |
6
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
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12 <!-- disabled error detection by exit code to be able to detect oom errors by |
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
1
diff
changeset
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13 regex, can be reenabled when https://github.com/galaxyproject/galaxy/pull/6338 is merged |
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
1
diff
changeset
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14 <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" /> |
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
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diff
changeset
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15 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />--> |
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
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changeset
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16 <regex match="Failed to allocate sufficient memory." source="stderr" level="fatal_oom" /> |
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
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diff
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17 <regex match=".+" source="stderr" level="fatal" description=""/> |
1
df7738595640
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents:
diff
changeset
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18 </stdio> |
df7738595640
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents:
diff
changeset
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19 </xml> |
df7738595640
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents:
diff
changeset
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20 |
df7738595640
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents:
diff
changeset
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21 <xml name="version_command"> |
df7738595640
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents:
diff
changeset
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22 <version_command>diamond version</version_command> |
df7738595640
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents:
diff
changeset
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23 </xml> |
df7738595640
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
bgruening
parents:
diff
changeset
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24 |
6
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
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changeset
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25 <xml name="output_type_macro"> |
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
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changeset
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26 <conditional name="output"> |
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
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27 <param argument="--outfmt" type="select" label="Format of output file " help=""> |
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
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28 <option value="0">BLAST pairwise</option> |
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
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changeset
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29 <option value="5">BLAST XML</option> |
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
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changeset
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30 <option value="6">BLAST tabular</option> |
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
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changeset
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31 <option value="100">DAA</option> |
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
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32 <option value="101">SAM</option> |
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
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33 <option value="102">Taxonomic classification</option> |
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
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changeset
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34 </param> |
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
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35 <when value="0"/> |
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
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changeset
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36 <when value="5"/> |
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
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changeset
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37 <when value="6"> |
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
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38 <param name="fields" type="select" label="Tabular fields" help="" multiple="true"> |
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
1
diff
changeset
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39 <option value="qseqid" selected="true">Query Seq - id</option> |
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
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diff
changeset
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40 <option value="sseqid" selected="true">Subject Seq - id</option> |
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
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41 <option value="sallseqid">All subject Seq - id(s)</option> |
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
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42 <option value="qlen">Query sequence length</option> |
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
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43 <option value="slen">Subject sequence length</option> |
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
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44 <option value="pident" selected="true">Percentage of identical matches</option> |
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
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45 <option value="length" selected="true">Alignment length</option> |
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
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46 <option value="nident">Number of identical matches</option> |
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
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47 <option value="mismatch" selected="true">Number of mismatches</option> |
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
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48 <option value="positive">Number of positive - scoring matches</option> |
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
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49 <option value="gapopen" selected="true">Number of gap openings</option> |
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
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50 <option value="gaps">Total number of gaps</option> |
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
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51 <option value="ppos">Percentage of positive - scoring matches</option> |
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
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52 <option value="qstart" selected="true">Start of alignment in query</option> |
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
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53 <option value="qend" selected="true">End of alignment in query</option> |
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
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54 <option value="sstart" selected="true">Start of alignment in subject</option> |
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
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55 <option value="send" selected="true">End of alignment in subject</option> |
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
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56 <option value="qseq">Aligned part of query sequence</option> |
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
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57 <option value="sseq">Aligned part of subject sequence</option> |
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
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58 <option value="evalue" selected="true">Expect value</option> |
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
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59 <option value="bitscore" selected="true">Bit score</option> |
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
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60 <option value="score">Raw score</option> |
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
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61 <option value="qframe">Query frame</option> |
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
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62 <option value="btop">Blast traceback operations(BTOP)</option> |
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
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63 <option value="staxids">unique Subject Taxonomy ID(s), separated by a ';' (in numerical order)</option> |
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
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64 <option value="stitle">Subject Title</option> |
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
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65 <option value="salltitles">All Subject Title(s)</option> |
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
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66 <option value="qcovhsp">Query Coverage Per HSP</option> |
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
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67 <option value="qtitle">Query title</option> |
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
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68 </param> |
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
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69 </when> |
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
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70 <when value="100"> |
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
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71 <param argument="--salltitles" type="boolean" truevalue="--salltitles" falsevalue="" checked="true" label="Include full subject titles in DAA file?" help=""/> |
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
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72 <param argument="--sallseqid" type="boolean" truevalue="--sallseqid" falsevalue="" checked="true" label="Include all subject ids in DAA file?" help=""/> |
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
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73 </when> |
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
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74 <when value="101"> |
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
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75 <param argument="--salltitles" type="boolean" truevalue="--salltitles" falsevalue="" checked="true" label="Include full subject titles in DAA file?" help=""/> |
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
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76 <param argument="--sallseqid" type="boolean" truevalue="--sallseqid" falsevalue="" checked="true" label="Include all subject ids in DAA file?" help=""/> |
64be1ac21109
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
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77 </when> |
64be1ac21109
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78 <when value="102"/> |
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79 </conditional> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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80 </xml> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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81 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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82 <xml name="hit_filter_macro"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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83 <conditional name="hit_filter"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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84 <param name="hit_filter_select" type="select" label="Method to restrict the number of hits?"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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85 <option value="max">Maximum number of target sequences</option> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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86 <option value="top">Percentage of top alignment score</option> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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87 </param> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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88 <when value="max"> |
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89 <param name="max_target_seqs" argument="--max-target-seqs" type="integer" value="25" label="The maximum number of target sequences per query to report alignments for" help="Setting this to 0 will report all alignments that were found." /> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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90 </when> |
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91 <when value="top"> |
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92 <param argument="--top" type="integer" value="0" label="Keep alignments within the given percentage range of the top alignment score for a query" help="For example, setting this to 10 will report all align- |
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93 ments whose score is at most 10% lower than the best alignment score for a query." /> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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94 </when> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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95 </conditional> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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96 </xml> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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97 |
1
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98 <xml name="citations"> |
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99 <citations> |
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100 <citation type="doi">10.1038/nmeth.3176</citation> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
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101 </citations> |
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102 </xml> |
6
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103 |
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104 |
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105 <xml name="output_macro"> |
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106 <data format="txt" name="blast_pairw" label="${tool.name} on ${on_string}"> |
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107 <filter>output["outfmt"] == "0"</filter> |
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108 </data> |
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109 <data format="xml" name="blast_xml" label="${tool.name} on ${on_string}"> |
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110 <filter>output["outfmt"] == "5"</filter> |
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111 </data> |
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112 <data format="tabular" name="blast_tabular" label="${tool.name} on ${on_string}"> |
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113 <filter>output["outfmt"] == "6"</filter> |
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114 </data> |
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115 <!-- for daa diamond appends the .daa extension -> hence from_work_dir --> |
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116 <data format="daa" name="daa_output" label="${tool.name} on ${on_string}" from_work_dir="output.daa"> |
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117 <filter>output["outfmt"] == "100"</filter> |
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118 </data> |
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119 <data format="sam" name="sam_output" label="${tool.name} on ${on_string}"> |
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120 <filter>output["outfmt"] == "101"</filter> |
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121 </data> |
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122 <data format="tabular" name="tax_output" label="${tool.name} on ${on_string}"> |
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123 <filter>output["outfmt"] == "102"</filter> |
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124 </data> |
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125 </xml> |
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126 |
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127 <token name="@OUTPUT_ARGS@"> |
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128 #if $output.outfmt == "0" |
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129 --outfmt '0' |
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130 --out '$blast_pairw' |
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131 #else if $output.outfmt == "5" |
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132 --outfmt '5' |
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133 --out '$blast_xml' |
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134 #else if $output.outfmt == "6" |
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135 --outfmt '6' #echo ' '.join(str($output.fields).split(',')) |
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136 --out '$blast_tabular' |
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137 #else if $output.outfmt == "100" |
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138 --outfmt '100' |
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139 --out output.daa |
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140 #else if $output.outfmt == "101" |
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141 --outfmt '101' |
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142 --out '$sam_output' |
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143 #else if $output.outfmt == "102" |
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144 --outfmt '102' |
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145 --out '$tax_output' |
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146 #end if |
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147 </token> |
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148 |
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149 <token name="@HITFILTER_ARGS@"> |
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150 #if str($hit_filter.hit_filter_select) == 'max': |
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151 --max-target-seqs '$hit_filter.max_target_seqs' |
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152 #else: |
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153 --top '$hit_filter.top' |
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154 #end if |
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155 </token> |
1
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156 </macros> |