annotate pear_stats.xml @ 0:ec62f17fcfe6 draft default tip

"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/pear_stats commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e"
author qfabrepo
date Mon, 14 Sep 2020 04:50:28 +0000
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1 <tool id="pearStat" name="PEAR Statistics" version="1.0.0">
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2 <description>Generate paired-end reads overlap Statistic from PEAR log file</description>
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3 <version_command>
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4 python ${__tool_directory__}/pear_stats.py --version
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5 </version_command>
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6 <command detect_errors="aggressive"><![CDATA[
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7 #set files=""
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8 #for $index,$file in enumerate($input):
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9 #set $files += str($file)+","
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10 #end for
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11 #set $files=$files[:-1]
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12
ec62f17fcfe6 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/pear_stats commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e"
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13 #set names=','.join( [ str( $name ) for $name in $input.keys() ])
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14
ec62f17fcfe6 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/pear_stats commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e"
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15 python $__tool_directory__/pear_stats.py -i "$files" -s "$names" -o $output
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16 ]]> </command>
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17 <inputs>
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18 <param name="input" type="data_collection" format="txt" collection_type="list" label="PEAR LOG FILE"/>
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19 </inputs>
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20 <outputs>
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21 <!--<data format="tabular" name="output" label="${tool.name}.${input.display_name}"/>-->
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22 <data format="tabular" name="output" label="${tool.name}.log"/>
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23 </outputs>
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24 <tests>
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25 <test>
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26 <param name="input">
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27 <collection type="list">
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28 <element name="F3D0" value="F3D0.log" />
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29 <element name="F3D1" value="F3D1.log" />
ec62f17fcfe6 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/pear_stats commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e"
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30 </collection>
ec62f17fcfe6 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/pear_stats commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e"
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31 </param>
ec62f17fcfe6 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/pear_stats commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e"
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32 <output name="output" file="test_output.txt"/>
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33 </test>
ec62f17fcfe6 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/pear_stats commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e"
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34 </tests>
ec62f17fcfe6 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/pear_stats commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e"
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35
ec62f17fcfe6 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/pear_stats commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e"
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36 <help>
ec62f17fcfe6 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/pear_stats commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e"
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37 ** what it does **
ec62f17fcfe6 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/pear_stats commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e"
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38
ec62f17fcfe6 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/pear_stats commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e"
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39 Creates summary log file by extracting "Assembled reads", "Discarded reads" and "Not assembled reads" from PEAR_ log.
ec62f17fcfe6 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/pear_stats commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e"
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40
ec62f17fcfe6 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/pear_stats commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e"
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41 .. _PEAR: https://sco.h-its.org/exelixis/web/software/pear/doc.html
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42
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43 -----
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44
ec62f17fcfe6 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/pear_stats commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e"
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45 =======
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46 Example
ec62f17fcfe6 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/pear_stats commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e"
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47 =======
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48
ec62f17fcfe6 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/pear_stats commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e"
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49 PEAR v0.9.6 [January 15, 2015]
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50
ec62f17fcfe6 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/pear_stats commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e"
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51 Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR
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52 Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593
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53
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54 ==================================== =======================================
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55 Field Parameter and output
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56 ------------------------------------ ---------------------------------------
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57 Forward reads file.................: /mnt/galaxy/files/014/dataset_14938.dat
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58 Reverse reads file.................: /mnt/galaxy/files/014/dataset_14939.dat
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59 PHRED..............................: 33
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60 Using empirical frequencies........: NO
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61 Statistical method.................: OES
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62 Maximum assembly length............: 999999
ec62f17fcfe6 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/pear_stats commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e"
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63 Minimum assembly length............: 50
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64 p-value............................: 0.010000
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65 Quality score threshold (trimming).: 0
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66 Minimum read size after trimming...: 1
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67 Maximal ratio of uncalled bases....: 1.000000
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68 Minimum overlap....................: 10
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69 Scoring method.....................: Scaled score
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70 Threads............................: 2
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71
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72 Allocating memory..................: 200,000,000 bytes
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73 Assemblying reads: 0%
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74 Assemblying reads: 100%
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75
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76 Assembled reads ...................: 906 / 990 (91.515%)
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77 Discarded reads ...................: 0 / 990 (0.000%)
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78 Not assembled reads ...............: 84 / 990 (8.485%)
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79 Assembled reads file...............: pear.assembled.fastq
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80 Discarded reads file...............: pear.discarded.fastq
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81 Unassembled forward reads file.....: pear.unassembled.forward.fastq
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82 Unassembled reverse reads file.....: pear.unassembled.reverse.fastq
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83 ==================================== =======================================
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84
ec62f17fcfe6 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/pear_stats commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e"
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85
ec62f17fcfe6 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/pear_stats commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e"
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86 -----
ec62f17fcfe6 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/pear_stats commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e"
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87
ec62f17fcfe6 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/pear_stats commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e"
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88 =========
ec62f17fcfe6 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/pear_stats commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e"
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89 Resources
ec62f17fcfe6 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/pear_stats commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e"
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90 =========
ec62f17fcfe6 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/pear_stats commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e"
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91
ec62f17fcfe6 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/pear_stats commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e"
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92 **Wrapper Authors**
ec62f17fcfe6 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/pear_stats commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e"
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93
ec62f17fcfe6 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/pear_stats commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e"
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94 QFAB Bioinformatics (support@qfab.org)
ec62f17fcfe6 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/pear_stats commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e"
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95
ec62f17fcfe6 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/pear_stats commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e"
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96 </help>
ec62f17fcfe6 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/pear_stats commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e"
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97 <citations>
ec62f17fcfe6 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/pear_stats commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e"
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98 <citation type="doi">10.1093/bioinformatics/btt593</citation>
ec62f17fcfe6 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/pear_stats commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e"
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99 </citations>
ec62f17fcfe6 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/pear_stats commit 0db3cb4e9a87400bb2f8402ffc23334e24ad4b4e"
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100 </tool>