Mercurial > repos > iuc > samtools_fastx

annotate samtools_fastx.xml @ 0:a0d039fa9771 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
author iuc
date Mon, 12 Mar 2018 12:53:10 -0400
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children a8d69aee190e
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0
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
iuc
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1 <?xml version="1.0"?>
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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2 <tool id="samtools_fastx" name="Samtools extract" version="@TOOL_VERSION@">
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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3 <description>FASTA or FASTQ from a SAM file</description>
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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4 <macros>
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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5 <import>macros.xml</import>
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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6 </macros>
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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7 <expand macro="requirements" />
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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8 <expand macro="version_command" />
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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9 <command detect_errors="exit_code">
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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10 <![CDATA[
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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11 samtools $output.output_format
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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12 #if $output.output_format == 'fastq':
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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13 -v $output.default_quality $output.output_quality
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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14 #end if
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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15 #if $reference:
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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16 --reference '$reference'
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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17 #end if
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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18 $copy_flags $omit_read_number
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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19 -0 '$nonspecific'
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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20 -1 '$forward'
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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21 -2 '$reverse'
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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22 #if str($inclusive_filter) != 'None':
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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23 #set $filter = $inclusive_filter
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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24 @FLAGS@
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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25 -f $flags
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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26 #end if
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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27 #if str($exclusive_filter) != 'None':
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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28 #set $filter = $exclusive_filter
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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29 @FLAGS@
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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30 -F $flags
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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31 #end if
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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32 '$input'
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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33 ]]>
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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34 </command>
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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35 <inputs>
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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36 <param name="input" type="data" format="bam,sam" label="BAM or SAM file to convert" />
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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37 <param argument="--reference" type="data" format="fasta" optional="True" label="Reference FASTA" />
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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38 <param name="copy_flags" argument="-t" type="boolean" truevalue="-t" falsevalue="" label="Copy RG/BC/QT flags to output header" />
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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39 <param name="omit_read_number" argument="-n" type="boolean" truevalue="-n" falsevalue="" label="Do not append /1 and /2 to read names" />
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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40 <param name="inclusive_filter" argument="-f" type="select" multiple="True" label="Require that these flags be set">
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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41 <expand macro="filter_options" />
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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42 </param>
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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43 <param name="exclusive_filter" argument="-F" type="select" multiple="True" label="Exclude reads with the following flags set">
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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44 <expand macro="filter_options" />
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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45 </param>
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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46 <conditional name="output">
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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47 <param name="output_format" type="select" label="Output format">
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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48 <option value="fasta">FASTA</option>
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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49 <option value="fastq">FASTQ</option>
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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50 </param>
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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51 <when value="fastq">
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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52 <param name="default_quality" argument="-v" type="integer" value="1" label="Default quality if none is given" />
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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53 <param name="output_quality" argument="-O" type="boolean" truevalue="-O" falsevalue="" label="Output quality in the OQ tag if available" />
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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54 </when>
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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55 <when value="fasta" />
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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56 </conditional>
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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57 </inputs>
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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58 <outputs>
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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59 <data name="nonspecific" format="fasta" label="${on_string} converted to ${output.output_format} (Neither or both)">
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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60 <change_format>
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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61 <when input="output_format" value="fastq" format="fastq" />
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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62 </change_format>
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63 </data>
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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64 <data name="forward" format="fasta" label="${on_string} converted to ${output.output_format} (READ1)">
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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65 <change_format>
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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66 <when input="output_format" value="fastq" format="fastq" />
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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67 </change_format>
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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68 </data>
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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69 <data name="reverse" format="fasta" label="${on_string} converted to ${output.output_format} (READ2)">
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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70 <change_format>
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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71 <when input="output_format" value="fastq" format="fastq" />
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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72 </change_format>
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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73 </data>
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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74 </outputs>
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75 <tests>
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76 <test>
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77 <param name="input" value="samtools_fastx-in1.bam" ftype="bam" />
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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78 <param name="output_format" value="fasta" />
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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79 <output name="nonspecific" file="samtools_fastx-out1-1.fasta" />
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80 <output name="forward" file="samtools_fastx-out1-2.fasta" />
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81 <output name="reverse" file="samtools_fastx-out1-3.fasta" />
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82 </test>
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83 <test>
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84 <param name="input" value="samtools_fastx-in2.bam" ftype="bam" />
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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85 <param name="output_format" value="fastq" />
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86 <output name="nonspecific" file="samtools_fastx-out2-1.fastq" />
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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87 <output name="forward" file="samtools_fastx-out2-2.fastq" />
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88 <output name="reverse" file="samtools_fastx-out2-3.fastq" />
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89 </test>
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90 <test>
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91 <param name="input" value="samtools_fastx-in3.sam" ftype="sam" />
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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92 <param name="output_format" value="fasta" />
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93 <output name="nonspecific" file="samtools_fastx-out3-1.fasta" />
a0d039fa9771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fastx commit 9291a5cc3e04c19cefb28b1431a71a619e5e85b4
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94 <output name="forward" file="samtools_fastx-out3-2.fasta" />
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95 <output name="reverse" file="samtools_fastx-out3-3.fasta" />
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96 </test>
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97 </tests>
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98 <help>
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99 <![CDATA[
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100 This tool uses `Samtools <http://www.htslib.org/>`_ to extract sequences from a SAM or BAM file in FASTA or FASTQ format.
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101 ]]>
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102 </help>
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103 <expand macro="citations" />
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104 </tool>