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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
author iuc
date Sun, 08 Sep 2024 03:24:55 +0000
parents a53efedba9e7
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1 <tool id="bam_to_sam" name="BAM-to-SAM" version="2.0.4" profile="@PROFILE@">
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2 <description>convert BAM to SAM</description>
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f57df915aa10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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4 <macros>
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5 <import>macros.xml</import>
f57df915aa10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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6 </macros>
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7 <expand macro="requirements"/>
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8 <expand macro="stdio"/>
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9 <expand macro="version_command"/>
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f57df915aa10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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11 <command><![CDATA[
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12 samtools view -o '${output1}' ${header} '${input1}'
f57df915aa10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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13 ]]></command>
f57df915aa10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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14
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15 <inputs>
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16 <param format="bam" name="input1" type="data" label="BAM File to Convert" />
f57df915aa10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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17 <param name="header" label="Header options" type="select"
f57df915aa10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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18 help="Allows to choose between seeing the entire dataset with the header, header only, or data only.">
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19 <option value="-h">Include header in SAM output (-h)</option>
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20 <option value="-H">Return header only (-H)</option>
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21 <option value="">Exclude header</option>
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22 </param>
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23 </inputs>
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24 <outputs>
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25 <data format="sam" label="${tool.name} on ${on_string}: converted SAM" name="output1" />
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26 </outputs>
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27 <tests>
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28 <test>
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29 <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" />
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30 <param name="header" value="-h" />
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10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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31 <output file="bam_to_sam_out1.sam" name="output1" lines_diff="2" />
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32 </test>
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33 <test>
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34 <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" />
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35 <param name="header" value="-H" />
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10184eaa85fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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36 <output file="bam_to_sam_out2.sam" name="output1" lines_diff="2" />
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37 </test>
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38 <test>
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39 <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" />
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40 <param name="header" value="" />
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f57df915aa10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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41 <output file="bam_to_sam_out3.sam" name="output1" />
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42 </test>
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43 </tests>
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44 <help><![CDATA[
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45 **What it does**
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46
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f57df915aa10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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47 Converts BAM dataset to SAM using the ``samtools view`` command.
f57df915aa10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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48 ]]></help>
f57df915aa10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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49 <expand macro="citations"/>
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50 </tool>