Mercurial > repos > tiagoantao > clone_filter
annotate STACKS_clone_filter.xml @ 12:7a8369cfa7c1 draft default tip
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author | tiagoantao |
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date | Wed, 10 Feb 2016 14:04:19 -0500 |
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1 <tool id="STACKS_clone_filter" name="STACKS: clone_filter" version="0.9.0"> |
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2 <description>Run the STACKS clone_filter program</description> |
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3 |
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4 |
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5 <requirements> |
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6 <requirement type="package" version="1.18">stacks</requirement> |
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7 </requirements> |
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8 |
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9 <stdio> |
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10 <exit_code range="1" level="fatal" description="Error in Stacks clone_filter" /> |
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11 </stdio> |
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12 |
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13 <command interpreter="python"> |
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14 STACKS_clone_filter.py |
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15 #if $data_type.dt_select == 'single': |
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16 -f $data_type.fname |
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17 #else |
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18 -fwd $data_type.fwd |
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19 -rev $data_type.rev |
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20 #end if |
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21 -opt $oligo_option |
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22 #if $oligo_len_1 > -1: |
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23 --oligo_len_1 $oligo_len_1 |
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24 #end if |
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25 #if $oligo_len_2 > -1: |
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26 --oligo_len_2 $oligo_len_2 |
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27 #end if |
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28 </command> |
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29 |
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30 <inputs> |
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31 <conditional name="data_type"> |
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32 <param name="dt_select" type="select" label="Single or Paired-end"> |
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33 <option value="single">Single</option> |
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34 <option value="pair">Pair</option> |
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35 </param> |
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36 <when value="single"> |
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37 <param name="fname" type="data" format="fastq" label="FASTQ" /> |
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38 </when> |
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39 <when value="pair"> |
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40 <param name="fwd" type="data" format="fastq" label="Forward FASTQ" /> |
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41 <param name="rev" type="data" format="fastq" label="Reverse FASTQ" /> |
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42 </when> |
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43 </conditional> |
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44 <param name="oligo_len_1" value="-1" type="integer" label="length of the single-end oligo sequence in data set (-1 == ignore)"/> |
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45 <param name="oligo_len_2" value="-1" type="integer" label="length of the paired-end oligo sequence in data set (-1 == ignore)"/> |
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46 <param name="oligo_option" type="select" label="Oligo sequence options"> |
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47 <option value="inline_null" selected="true">random oligo is inline with sequence, occurs only on single-end read</option> |
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48 <option value="null_index">random oligo is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided).</option> |
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49 <option value="index_null">random oligo is provded in FASTQ header (Illumina i5 or i7 read)</option> |
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50 <option value="inline_inline">random oligo is inline with sequence, occurs on single and paired-end read</option> |
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51 <option value="index_index">random oligo is provded in FASTQ header (Illumina i5 and i7 read)</option> |
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52 <option value="inline_index">random oligo is inline with sequence on single-end read and second oligo occurs in FASTQ header</option> |
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53 <option value="index_inline">random oligo occurs in FASTQ header (Illumina i5 or i7 read) and is inline with sequence on single-end read (if single read data) or paired-end read (if paired data)</option> |
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54 </param> |
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55 </inputs> |
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56 |
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57 <outputs> |
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58 <data format="fastq" name="clean" from_work_dir="job_outputs/clean.fq"> |
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59 <filter>data_type['dt_select'] == 'single' </filter> |
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60 </data> |
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61 <data format="fastq" name="clean_fwd" from_work_dir="job_outputs/fwd.fq"> |
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62 <filter>data_type['dt_select'] == 'pair' </filter> |
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63 </data> |
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64 <data format="fastq" name="clean_rev" from_work_dir="job_outputs/rev.fq"> |
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65 <filter>data_type['dt_select'] == 'pair' </filter> |
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66 </data> |
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67 </outputs> |
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68 |
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69 <tests> |
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70 <test> |
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71 <param name="dt_select" value="pair" /> |
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72 <param name="fwd" value="fwd.fq" /> |
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73 <param name="rev" value="rev.fq" /> |
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74 <output name="clean_fwd" /> |
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75 <output name="clean_rev" /> |
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76 </test> |
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77 </tests> |
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78 |
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79 <help> |
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80 -------- |
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81 |
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82 **Project links:** |
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83 |
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84 `STACKS website <http://creskolab.uoregon.edu/stacks/>`_ . |
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85 |
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86 `STACKS manual <http://creskolab.uoregon.edu/stacks/stacks_manual.pdf>`_ . |
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87 |
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88 `STACKS google group <https://groups.google.com/forum/#!forum/stacks-users>`_ . |
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89 |
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90 </help> |
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91 <citations> |
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92 <citation type="doi">10.1111/mec.12354</citation> |
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93 <citation type="doi">10.1111/mec.12330</citation> |
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94 <citation type="doi">10.1534/g3.111.000240</citation> |
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95 <citation type="doi">10.1534/genetics.111.127324</citation> |
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96 <citation type="doi">10.1111/j.1755-0998.2010.02967.x</citation> |
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97 <citation type="doi">10.1073/pnas.1006538107</citation> |
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98 </citations> |
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99 </tool> |