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annotate fastx_quality_statistics.xml @ 3:59003d0543cd draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
author iuc
date Tue, 08 May 2018 13:28:00 -0400
parents 7306ec78632a
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59003d0543cd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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1 <tool id="cshl_fastx_quality_statistics" version="1.0.1" name="Compute quality statistics">
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2 <description></description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
59003d0543cd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
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8 @CATS@ fastx_quality_stats
59003d0543cd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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9 -o '$output'
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10 @FQQUAL@
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11 ]]></command>
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12
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13 <inputs>
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14 <expand macro="fastq_input" />
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15 </inputs>
7306ec78632a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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16 <outputs>
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17 <data name="output" format="txt" metadata_source="input" />
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18 </outputs>
7306ec78632a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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19 <tests>
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20 <test>
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21 <param name="input" value="fastq_stats1.fastq" ftype="fastqsanger"/>
7306ec78632a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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22 <output name="output" file="fastq_stats1.out" />
7306ec78632a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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23 </test>
7306ec78632a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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24 </tests>
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59003d0543cd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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25 <help><![CDATA[
0
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26 **What it does**
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27
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28 Creates quality statistics report for the given Solexa/FASTQ library.
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29
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30 .. class:: infomark
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31
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32 **TIP:** This statistics report can be used as input for **Quality Score** and **Nucleotides Distribution** tools.
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33
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34 -----
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35
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36 **The output file will contain the following fields:**
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37
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38 * column = column number (1 to 36 for a 36-cycles read Solexa file)
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39 * count = number of bases found in this column.
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40 * min = Lowest quality score value found in this column.
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41 * max = Highest quality score value found in this column.
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42 * sum = Sum of quality score values for this column.
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43 * mean = Mean quality score value for this column.
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44 * Q1 = 1st quartile quality score.
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45 * med = Median quality score.
7306ec78632a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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46 * Q3 = 3rd quartile quality score.
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47 * IQR = Inter-Quartile range (Q3-Q1).
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48 * lW = 'Left-Whisker' value (for boxplotting).
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49 * rW = 'Right-Whisker' value (for boxplotting).
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50 * A_Count = Count of 'A' nucleotides found in this column.
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51 * C_Count = Count of 'C' nucleotides found in this column.
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52 * G_Count = Count of 'G' nucleotides found in this column.
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53 * T_Count = Count of 'T' nucleotides found in this column.
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54 * N_Count = Count of 'N' nucleotides found in this column.
0
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55
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56 For example::
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57
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58 1 6362991 -4 40 250734117 39.41 40 40 40 0 40 40 1396976 1329101 678730 2958184 0
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59 2 6362991 -5 40 250531036 39.37 40 40 40 0 40 40 1786786 1055766 1738025 1782414 0
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60 3 6362991 -5 40 248722469 39.09 40 40 40 0 40 40 2296384 984875 1443989 1637743 0
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61 4 6362991 -4 40 248214827 39.01 40 40 40 0 40 40 2536861 1167423 1248968 1409739 0
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62 36 6362991 -5 40 117158566 18.41 7 15 30 23 -5 40 4074444 1402980 63287 822035 245
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63
0
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64 ------
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65
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66 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
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67
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68 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
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69 ]]></help>
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70 <expand macro="citations" />
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71 <!-- FASTQ-Statistics is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
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72 </tool>