Mercurial > repos > iuc > idba_hybrid
annotate idba_hybrid.xml @ 2:5c5806e23338 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 9c0a7395ca18043ae2dd957f39f47b65c938750a
author | iuc |
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date | Thu, 21 Jul 2022 13:35:37 +0000 |
parents | a81c5169e9fc |
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rev | line source |
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0
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
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changeset
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1 <tool id="idba_hybrid" name="IDBA-HYBRID" version="@IDBA_VERSION@"> |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
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2 <description> |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
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3 Iterative de Bruijn Graph Assembler for hybrid sequencing data |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff
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4 </description> |
2
5c5806e23338
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 9c0a7395ca18043ae2dd957f39f47b65c938750a
iuc
parents:
0
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5 <expand macro="bio_tools"/> |
0
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
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6 <macros> |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
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7 <import>macros.xml</import> |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
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8 </macros> |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff
changeset
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9 <expand macro="requirements"/> |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
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10 <command detect_errors="aggressive"><![CDATA[ |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
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11 idba_hybrid |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
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12 |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
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13 @MAIN_INPUT@ |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
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14 #if $ref_source.ref_source_sel == "cached" |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
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15 --reference '${$ref_source.reference.fields.path}' |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
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16 #else |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
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17 --reference '$ref_source.reference' |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
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18 #end if |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
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19 @LEVELS_INPUT@ |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff
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20 @KMER_OPTIONS@ |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
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21 @FILTER_OPTIONS@ |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff
changeset
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22 --min_region $min_region |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff
changeset
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23 --max_gap $max_gap |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff
changeset
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24 @MIN_PAIRS_FILTER@ |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
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25 @OTHER_OPTIONS@ |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
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26 @THREADS@ |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
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27 ]]></command> |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
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28 |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff
changeset
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29 <inputs> |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff
changeset
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30 <expand macro="main_input"/> |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
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changeset
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31 <conditional name="ref_source"> |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff
changeset
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32 <param label="Choose the source for the reference genome" name="ref_source_sel" type="select"> |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
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33 <option value="cached">Locally cached</option> |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
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changeset
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34 <option value="history">History</option> |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
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35 </param> |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
diff
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36 <when value="cached"> |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
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37 <param argument="--reference" label="Using reference genome" type="select"> |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
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38 <options from_data_table="all_fasta"> |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
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39 <filter column="1" type="sort_by" /> |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
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40 </options> |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
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41 <validator message="No reference genome is available" type="no_options" /> |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
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42 </param> |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
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43 </when> |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
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44 <when value="history"> |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
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45 <param argument="--reference" type="data" format="fasta" label="Reference Annotation" /> |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
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46 </when> |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
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47 </conditional> |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
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48 <expand macro="levels_input"/> |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
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49 <expand macro="kmer_options" maxk_default="100" step_default="20"/> |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
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50 <expand macro="filter_options"/> |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
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51 <param argument="--min_region" type="integer" value="300" label="Minimum size of region in reference genome"/> |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
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52 <param argument="--max_gap" type="integer" value="3" label="Maximum gap in reference"/> |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
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53 <expand macro="min_pairs_filter"/> |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
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54 <expand macro="other_options"/> |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
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55 </inputs> |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
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56 <outputs> |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
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57 <data name="output" from_work_dir="out/scaffold.fa" format="fasta"/> |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
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58 </outputs> |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
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59 <tests> |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
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60 <!-- basic test + check of defaults --> |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
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61 <test> |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
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62 <param name="ref_source|reference" value="reference.fa" ftype="fasta"/> |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
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63 <param name="ref_source|ref_source_sel" value="history"/> |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
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64 <param name="read" value="merged.fa" ftype="fasta"/> |
2
5c5806e23338
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 9c0a7395ca18043ae2dd957f39f47b65c938750a
iuc
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0
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65 <output name="output" file="out/scaffold.fa" ftype="fasta" compare="re_match"/> |
0
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
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66 <assert_command> |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
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67 <has_text text="--min_region 300" /> |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
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68 <has_text text="--max_gap 3" /> |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
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69 </assert_command> |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
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70 </test> |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
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71 <!-- chached reference test --> |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
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72 <test> |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
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73 <param name="ref_source|reference" value="test_id"/> |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
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74 <param name="ref_source|ref_source_sel" value="cached"/> |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
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75 <param name="read" value="merged.fa" ftype="fasta"/> |
2
5c5806e23338
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 9c0a7395ca18043ae2dd957f39f47b65c938750a
iuc
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0
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76 <output name="output" file="out/scaffold.fa" ftype="fasta" compare="re_match"/> |
0
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
parents:
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77 </test> |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
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78 <!-- tool specific parameters --> |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
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79 <test> |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
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80 <param name="ref_source|reference" value="reference.fa" ftype="fasta"/> |
a81c5169e9fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
iuc
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81 <param name="ref_source|ref_source_sel" value="history"/> |
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82 <param name="read" value="merged.fa" ftype="fasta"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
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83 <param name="min_region" value="299"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
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84 <param name="max_gap" value="2"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
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85 <assert_command> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
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86 <has_text text="--min_region 299" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
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87 <has_text text="--max_gap 2" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
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88 </assert_command> |
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89 <output name="output" file="out/scaffold.fa" ftype="fasta" compare="re_match"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 61e1699e65d6fd9f4f73650ed8463b37cd701344
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90 </test> |
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91 </tests> |
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92 <expand macro="help" more_help="IDBA-Hybrid is an iterative De Bruijn Graph De Novo Assembler for hybrid sequencing. It is an extension of IDBA-UD algorithm. It aims at using a closed related reference genome to help de novo assembly, especially when sequencing depth is low. IDBA-Hybrid does alignment between reads and reference first to extract similar regions in the reference genome, and then it correct the similar regions based on the alignment results and apply local assembly technique to resolve potential structure virations. Finally, it groups all the reads and the contigs got from those similar regions to do de novo assembly. The expriments showed it outperforms all existing de novo or hybrid assembly algorithms, especilly when the sequencing depth is low and the reference genome is similar to the target genome."/> |
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93 <expand macro="citations"> |
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94 </expand> |
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95 </tool> |