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annotate idba_tran.xml @ 1:33f00ff1cb22 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 665baeb11498ceef8abb1f1da43fe315d2d75b37"
author iuc
date Tue, 04 Aug 2020 05:51:17 -0400
parents a30d991a3fdd
children 03de4e0f84c2
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33f00ff1cb22 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud commit 665baeb11498ceef8abb1f1da43fe315d2d75b37"
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1 <tool id="idba_tran" name="IDBA-TRAN" version="@IDBA_VERSION@+galaxy0">
0
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2 <description>
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3 Iterative de Bruijn Graph Assembler for transcriptome data
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4 </description>
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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="requirements"/>
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9 <command detect_errors="aggressive"><![CDATA[
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10 idba_tran
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11
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12 @MAIN_INPUT@
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13 @KMER_OPTIONS@
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14 @FILTER_OPTIONS@
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15 --min_transcript $min_transcript
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16 --max_isoforms $max_isoforms
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17 --max_component_size $max_component_size
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18 @OTHER_OPTIONS@
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19 @THREADS@
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20 ]]></command>
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21 <inputs>
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22 <expand macro="main_input"/>
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23 <expand macro="kmer_options" maxk_default="60" step_default="10"/>
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24 <expand macro="filter_options"/>
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25 <param argument="--min_transcript" type="integer" value="300" label="Minimum size of transcript"/>
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26 <param argument="--max_isoforms" type="integer" value="3" label="Maximum number of isoforms"/>
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27 <param argument="--max_component_size" type="integer" value="30" label="Maximum size of component"/>
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28 <expand macro="other_options"/>
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29 </inputs>
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30 <outputs>
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31 <data name="output" from_work_dir="out/contig.fa" format="fasta"/>
0
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32 </outputs>
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33 <tests>
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34 <!-- basic test + tool specific defaults -->
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35 <test>
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36 <param name="read" value="merged.fa" ftype="fasta"/>
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37 <assert_command>
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38 <has_text text="--maxk 60" />
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39 <has_text text="--step 10" />
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40 <has_text text="--min_transcript 300" />
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41 <has_text text="--max_isoforms 3" />
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42 <has_text text="--max_component_size 30" />
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43 </assert_command>
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44 <output name="output" file="out/contig.fa" ftype="fasta" lines_diff="2"/>
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45 </test>
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46 <!-- tool specific parameters -->
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47 <test>
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48 <param name="read" value="merged.fa" ftype="fasta"/>
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49 <param name="min_transcript" value="299"/>
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50 <param name="max_isoforms" value="2"/>
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51 <param name="max_component_size" value="29"/>
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52 <assert_command>
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53 <has_text text="--min_transcript 299" />
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54 <has_text text="--max_isoforms 2" />
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55 <has_text text="--max_component_size 29" />
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56 </assert_command>
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57 <output name="output" file="out/contig.fa" ftype="fasta" lines_diff="2"/>
0
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58 </test>
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59 </tests>
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60 <expand macro="help" more_help="IDBA-Tran is an iterative De Bruijn Graph De Novo short read assembler for transcriptome. It is purely de novo assembler based on only RNA sequencing reads. IDBA-Tran uses local assembly to reconstructing missing k-mers in low-expressed transcripts and then employs progressive cutoff on contigs to seperate the graph into components. Each component corresponds to one gene in most cases and contains not many transcripts. A heuristic algorithm based on pair-end reads is then used to find the isoforms."/>
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61 <expand macro="citations">
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62 <citation type="doi">10.1093/bioinformatics/btt219</citation>
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63 </expand>
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64 </tool>