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annotate fastx_nucleotides_distribution.xml @ 4:21796f46e0ba draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
author iuc
date Tue, 08 May 2018 13:27:48 -0400
parents 9353010b95df
children ad116ae3f4d9
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4
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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1 <tool id="cshl_fastx_nucleotides_distribution" version="1.0.1" name="Draw nucleotides distribution chart">
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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2 <description></description>
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iuc
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3 <macros>
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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4 <import>macros.xml</import>
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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5 </macros>
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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6 <expand macro="requirements" />
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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7 <command detect_errors="exit_code"><![CDATA[
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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8 fastx_nucleotide_distribution_graph.sh
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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9 -t '$input.name'
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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10 -i '$input'
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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11 -o '$output'
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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12 ]]></command>
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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13 <inputs>
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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14 <param name="input" type="data" format="txt" label="Statistics text file" help="Output of 'FASTX Statistics' tool" />
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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15 </inputs>
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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16 <outputs>
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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17 <data name="output" format="png" metadata_source="input" />
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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18 </outputs>
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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19 <tests>
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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20 <test>
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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21 <param name="input" value="fastx_nucleotides_distribution-in1.txt" />
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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22 <output name="output" file="fastx_nucleotides_distribution-out1.png" compare="sim_size" delta="512" />
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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23 </test>
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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24 </tests>
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution 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 a stacked-histogram graph for the nucleotide distribution in the Solexa library.
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29
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30 .. class:: infomark
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31
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32 **TIP:** Use the **FASTQ Statistics** tool to generate the report file needed for this tool.
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33
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34 -----
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35
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36 **Output Examples**
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37
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38 The following chart clearly shows the barcode used at the 5'-end of the library: **GATCT**
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39
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40 .. image:: fastq_nucleotides_distribution_1.png
4
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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41
0
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42 In the following chart, one can almost 'read' the most abundant sequence by looking at the dominant values: **TGATA TCGTA TTGAT GACTG AA...**
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43
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44 .. image:: fastq_nucleotides_distribution_2.png
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45
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46 The following chart shows a growing number of unknown (N) nucleotides towards later cycles (which might indicate a sequencing problem):
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47
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48 .. image:: fastq_nucleotides_distribution_3.png
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49
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50 But most of the time, the chart will look rather random:
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51
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52 .. image:: fastq_nucleotides_distribution_4.png
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53
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54 ------
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55
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56 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
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57
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58 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
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59 ]]></help>
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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60 <expand macro="citations" />
21796f46e0ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_nucleotides_distribution commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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61 <!-- FASTQ-Nucleotides-Distribution is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
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62 </tool>