Mercurial > repos > devteam > fastq_quality_converter

annotate macros.xml @ 2:54053ea6c77e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
author iuc
date Tue, 08 May 2018 13:26:24 -0400
parents
children 045f0e1043f7
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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2
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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2 <macros>
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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3 <token name="@CATS@">
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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4 #if $input.is_of_type('fasta.gz', 'fastqsanger.gz', 'fastqsolexa.gz', 'fastqillumina.gz'):
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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5 zcat -f '$input' |
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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6 #elif $input.is_of_type('fastqsanger.bz2', 'fastqsolexa.bz2', 'fastqillumina.bz2'):
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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7 bzcat -f '$input' |
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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8 #else:
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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9 cat '$input' |
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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10 #end if
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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11 </token>
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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12 <token name="@FQQUAL@">
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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13 <![CDATA[
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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14 #if $input.is_of_type('fastqsanger', 'fastqsanger.gz', 'fastqsanger.bz2'):
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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15 -Q 33
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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16 #elif $input.is_of_type('fastqsolexa', 'fastqsolexa.gz', 'fastqsolexa.bz2', 'fastqillumina', 'fastqillumina.gz', 'fastqillumina.bz2'):
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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17 -Q 64
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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18 #end if
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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19 ]]>
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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20 </token>
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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21 <xml name="requirements">
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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22 <requirements>
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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23 <requirement type="package" version="@VERSION@">fastx_toolkit</requirement>
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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24 <yield />
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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25 </requirements>
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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26 </xml>
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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27 <token name="@VERSION@">0.0.14</token>
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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28 <token name="@SANGER@">fastqsanger,fastqsanger.gz,fastqsanger.bz2</token>
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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29 <token name="@SOLEXA@">fastqsolexa,fastqsolexa.gz,fastqsolexa.bz2</token>
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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30 <token name="@ILLUMINA@">fastqillumina,fastqillumina.gz,fastqillumina.bz2</token>
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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31 <token name="@FASTQS@">@SANGER@,@SOLEXA@,@ILLUMINA@</token>
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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32 <token name="@FASTAS@">fasta,fasta.gz</token>
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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33 <xml name="citations">
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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34 <citations>
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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35 <citation type="bibtex">
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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36 @UNPUBLISHED{agordon,
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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37 author = "Assaf Gordon",
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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38 title = "FASTQ/A short-reads pre-processing tools",
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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39 year = "2010",
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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40 note = "http://hannonlab.cshl.edu/fastx_toolkit/",
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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41 url = "http://hannonlab.cshl.edu/fastx_toolkit/"}
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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42 </citation>
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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43 </citations>
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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44 </xml>
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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45 <xml name="fasta_input">
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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46 <param name="input" type="data" format="@FASTAS@" label="Input FASTA file" />
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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47 </xml>
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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48 <xml name="fastq_input">
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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49 <param name="input" type="data" format="@FASTQS@" label="Input FASTQ file" />
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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50 </xml>
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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51 <xml name="fastx_input">
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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52 <param name="input" type="data" format="@FASTAS@,@FASTQS@" label="Input file in FASTA or FASTQ format" />
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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53 </xml>
54053ea6c77e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_converter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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54 </macros>