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annotate fastq_stats.xml @ 4:f0e7deab6518 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
author iuc
date Wed, 19 Feb 2020 12:34:52 -0500
parents b1cea1b2fcd0
children f86c27295151
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f0e7deab6518 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
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1 <tool id="fastq_stats" name="FASTQ Summary Statistics" version="@TOOL_VERSION@">
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2 <description>by column</description>
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f0e7deab6518 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
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3 <macros>
f0e7deab6518 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
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4 <import>macros.xml</import>
f0e7deab6518 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
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5 </macros>
f0e7deab6518 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
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6 <expand macro="requirements"/>
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b1cea1b2fcd0 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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7 <edam_topics>
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8 <edam_topic>topic_0622</edam_topic>
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9 </edam_topics>
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10 <edam_operations>
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11 <edam_operation>operation_3180</edam_operation>
b1cea1b2fcd0 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_stats commit 31edb920789fbd080260f853bc856be72fa7cfa8"
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12 </edam_operations>
2
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13 <command><![CDATA[
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14 gx-fastq-stats '$input_file' '$output_file' '${input_file.extension[len('fastq'):]}'
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15 ]]></command>
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16 <inputs>
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17 <param name="input_file" type="data" format="fastqsanger,fastqillumina,fastqsolexa,fastqcssanger,fastqsanger.gz,fastqillumina.gz,fastqsolexa.gz,fastqcssanger.gz,fastqsanger.bz2,fastqillumina.bz2,fastqsolexa.bz2,fastqcssanger.bz2" label="FASTQ File"/>
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18 </inputs>
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19 <outputs>
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20 <data name="output_file" format="tabular" />
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21 </outputs>
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22 <tests>
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23 <test>
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24 <param name="input_file" value="fastq_stats1.fastq" ftype="fastqsanger" />
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25 <output name="output_file" file="fastq_stats_1_out.tabular" />
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26 </test>
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27 </tests>
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28 <help><![CDATA[
1
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29 **What is does**
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30
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31 This tool creates summary statistics on a FASTQ file.
0
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32
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33 .. class:: infomark
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34
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35 **TIP:** This statistics report can be used as input for the **Boxplot** tools.
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36
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37 -----
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38
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39 **The output file will contain the following fields:**
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40
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41 * column = column number (1 to 36 for a 36-cycles read Solexa file)
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42 * count = number of bases found in this column.
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43 * min = Lowest quality score value found in this column.
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44 * max = Highest quality score value found in this column.
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45 * sum = Sum of quality score values for this column.
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46 * mean = Mean quality score value for this column.
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47 * Q1 = 1st quartile quality score.
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48 * med = Median quality score.
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49 * Q3 = 3rd quartile quality score.
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50 * IQR = Inter-Quartile range (Q3-Q1).
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51 * lW = 'Left-Whisker' value (for boxplotting).
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52 * rW = 'Right-Whisker' value (for boxplotting).
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53 * outliers = Scores falling beyond the left and right whiskers (comma separated list).
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54 * A_Count = Count of 'A' nucleotides found in this column.
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55 * C_Count = Count of 'C' nucleotides found in this column.
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56 * G_Count = Count of 'G' nucleotides found in this column.
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57 * T_Count = Count of 'T' nucleotides found in this column.
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58 * N_Count = Count of 'N' nucleotides found in this column.
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59 * Other_Nucs = Comma separated list of other nucleotides found in this column.
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60 * Other_Count = Comma separated count of other nucleotides found in this column.
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61
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62 For example::
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63
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64 #column count min max sum mean Q1 med Q3 IQR lW rW outliers A_Count C_Count G_Count T_Count N_Count other_bases other_base_count
2
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65 1 14336356 2 33 450600675 31.4306281875 32.0 33.0 33.0 1.0 31 33 2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30 4482314 2199633 4425957 3208745 19707
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66 2 14336356 2 34 441135033 30.7703737965 30.0 33.0 33.0 3.0 26 34 2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25 4419184 2170537 4627987 3118567 81
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67 3 14336356 2 34 433659182 30.2489127642 29.0 32.0 33.0 4.0 23 34 2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22 4310988 2941988 3437467 3645784 129
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68 4 14336356 2 34 433635331 30.2472490917 29.0 32.0 33.0 4.0 23 34 2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22 4110637 3007028 3671749 3546839 103
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69 5 14336356 2 34 432498583 30.167957813 29.0 32.0 33.0 4.0 23 34 2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22 4348275 2935903 3293025 3759029 124
0
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71 -----
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72
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73 .. class:: warningmark
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74
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75 Adapter bases in color space reads are excluded from statistics.
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76 ]]></help>
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77 <citations>
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78 <citation type="doi">10.1093/bioinformatics/btq281</citation>
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79 </citations>
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80 </tool>