Mercurial > repos > iuc > bam2fastx

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk commit 25e0d36ddaf6a61b41c6412ddc9865163f3875f6
author iuc
date Mon, 10 Mar 2025 16:09:44 +0000
parents 56d9933d2737
children
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56d9933d2737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk commit 7f0e2a6739769971f60c9719f1ef883c621d5ce1
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1 <tool id="bam2fastx" name="PacBio bam2fastx" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01">
56d9933d2737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk commit 7f0e2a6739769971f60c9719f1ef883c621d5ce1
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2 <description>PacBio BAM to Fastx</description>
56d9933d2737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk commit 7f0e2a6739769971f60c9719f1ef883c621d5ce1
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3 <macros>
1
df0fa70d83e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk commit 25e0d36ddaf6a61b41c6412ddc9865163f3875f6
iuc
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4 <token name="@TOOL_VERSION@">3.5.0</token>
0
56d9933d2737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk commit 7f0e2a6739769971f60c9719f1ef883c621d5ce1
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5 <token name="@VERSION_SUFFIX@">0</token>
56d9933d2737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk commit 7f0e2a6739769971f60c9719f1ef883c621d5ce1
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6 </macros>
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7 <requirements>
56d9933d2737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk commit 7f0e2a6739769971f60c9719f1ef883c621d5ce1
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8 <requirement type="package" version="@TOOL_VERSION@">pbtk</requirement>
56d9933d2737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk commit 7f0e2a6739769971f60c9719f1ef883c621d5ce1
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9 </requirements>
56d9933d2737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk commit 7f0e2a6739769971f60c9719f1ef883c621d5ce1
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10 <command><![CDATA[
56d9933d2737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk commit 7f0e2a6739769971f60c9719f1ef883c621d5ce1
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11 mkdir -p output_files/ &&
56d9933d2737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk commit 7f0e2a6739769971f60c9719f1ef883c621d5ce1
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12 ln -s '$input_bam' input.bam &&
56d9933d2737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk commit 7f0e2a6739769971f60c9719f1ef883c621d5ce1
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13 pbindex input.bam &&
56d9933d2737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk commit 7f0e2a6739769971f60c9719f1ef883c621d5ce1
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14 #if $output_format == "fasta_gz":
56d9933d2737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk commit 7f0e2a6739769971f60c9719f1ef883c621d5ce1
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15 bam2fasta -o output
56d9933d2737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk commit 7f0e2a6739769971f60c9719f1ef883c621d5ce1
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16 #elif $output_format == "fastq_gz":
56d9933d2737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk commit 7f0e2a6739769971f60c9719f1ef883c621d5ce1
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17 bam2fastq -o output
56d9933d2737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk commit 7f0e2a6739769971f60c9719f1ef883c621d5ce1
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18 #end if
56d9933d2737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk commit 7f0e2a6739769971f60c9719f1ef883c621d5ce1
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19 input.bam
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20 --num-threads "\${GALAXY_SLOTS:-1}" &&
56d9933d2737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk commit 7f0e2a6739769971f60c9719f1ef883c621d5ce1
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21 #if $output_format == "fasta_gz":
56d9933d2737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk commit 7f0e2a6739769971f60c9719f1ef883c621d5ce1
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22 mv output.fasta.gz '$output_fasta_gz'
56d9933d2737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk commit 7f0e2a6739769971f60c9719f1ef883c621d5ce1
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23 #elif $output_format == "fastq_gz":
56d9933d2737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk commit 7f0e2a6739769971f60c9719f1ef883c621d5ce1
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24 mv output.fastq.gz '$output_fastq_gz'
56d9933d2737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk commit 7f0e2a6739769971f60c9719f1ef883c621d5ce1
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25 #end if
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26 ]]></command>
56d9933d2737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk commit 7f0e2a6739769971f60c9719f1ef883c621d5ce1
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27 <inputs>
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28 <param name="input_bam" type="data" format="unsorted.bam" label="PacBio Bam file "/>
56d9933d2737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk commit 7f0e2a6739769971f60c9719f1ef883c621d5ce1
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29 <param name="output_format" type="select" label="Output Format" help="Output a fasta.gz or fastq.gz">
56d9933d2737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk commit 7f0e2a6739769971f60c9719f1ef883c621d5ce1
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30 <option value="fastq_gz">fastq.gz</option>
56d9933d2737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk commit 7f0e2a6739769971f60c9719f1ef883c621d5ce1
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31 <option value="fasta_gz">fasta.gz</option>
56d9933d2737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk commit 7f0e2a6739769971f60c9719f1ef883c621d5ce1
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32 </param>
56d9933d2737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk commit 7f0e2a6739769971f60c9719f1ef883c621d5ce1
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33 </inputs>
56d9933d2737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk commit 7f0e2a6739769971f60c9719f1ef883c621d5ce1
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34 <outputs>
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35 <data name="output_fasta_gz" format="fasta.gz" label="${tool.name} on ${on_string}: Fasta">
56d9933d2737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk commit 7f0e2a6739769971f60c9719f1ef883c621d5ce1
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36 <filter>output_format == "fasta_gz"</filter>
56d9933d2737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk commit 7f0e2a6739769971f60c9719f1ef883c621d5ce1
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37 </data>
56d9933d2737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk commit 7f0e2a6739769971f60c9719f1ef883c621d5ce1
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38 <data name="output_fastq_gz" format="fastqsanger.gz" label="${tool.name} on ${on_string}: Fastq">
56d9933d2737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk commit 7f0e2a6739769971f60c9719f1ef883c621d5ce1
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39 <filter>output_format == "fastq_gz"</filter>
56d9933d2737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk commit 7f0e2a6739769971f60c9719f1ef883c621d5ce1
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40 </data>
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41 </outputs>
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42 <tests>
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43 <test expect_num_outputs="1">
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44 <param name="input_bam" ftype="unsorted.bam" value="sample.bam"/>
56d9933d2737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk commit 7f0e2a6739769971f60c9719f1ef883c621d5ce1
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45 <param name="output_format" value="fastq.gz" />
56d9933d2737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk commit 7f0e2a6739769971f60c9719f1ef883c621d5ce1
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46 <output name="output_fastq_gz" decompress="true">
56d9933d2737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk commit 7f0e2a6739769971f60c9719f1ef883c621d5ce1
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47 <assert_contents>
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48 <has_text text="AATGCCTTATTAAGTTAAGAAATGGTTTTTTTTAAACTTACAGATGGAA" />
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49 </assert_contents>
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50 </output>
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51 </test>
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52 <test expect_num_outputs="1" >
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53 <param name="input_bam" ftype="bam" value="sample.bam"/>
56d9933d2737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk commit 7f0e2a6739769971f60c9719f1ef883c621d5ce1
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54 <param name="output_format" value="fasta.gz" />
56d9933d2737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk commit 7f0e2a6739769971f60c9719f1ef883c621d5ce1
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55 <output name="output_fasta_gz" decompress="true">
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56 <assert_contents>
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57 <has_text text="AATGCCTTATTAAGTTAAGAAATGGTTTTTTTTAAACTTACAGATGGAA" />
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58 </assert_contents>
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59 </output>
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60 </test>
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61 </tests>
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62 <help><![CDATA[
56d9933d2737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk commit 7f0e2a6739769971f60c9719f1ef883c621d5ce1
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63 Convert a PacBio BAM file to Fastq or Fasta file.
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64 ]]></help>
56d9933d2737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pbtk commit 7f0e2a6739769971f60c9719f1ef883c621d5ce1
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65 <citations>
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66 <citation type="bibtex">
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67 @misc{githubpbtk,
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68 author = {},
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69 year = {2024},
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70 title = {pbtk},
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71 publisher = {GitHub},
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72 journal = {GitHub repository},
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73 url = {https://github.com/PacificBiosciences/pbtk},
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74 }
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75 </citation>
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76 </citations>
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77 </tool>