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1 <tool id="bam_to_sam" name="BAM-to-SAM" version="1.0.6">
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2 <macros>
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3 <import>macros.xml</import>
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4 </macros>
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5 <expand macro="requirements"></expand>
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6 <expand macro="version_command"></expand>
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7 <expand macro="stdio"></expand>
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8 <description>converts BAM format to SAM format</description>
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9 <command>
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10 <![CDATA[
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11 samtools sort -O bam -@ \${GALAXY_SLOTS:-1} "$input1" -o sorted_input.bam -T temp &&
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12 samtools view sorted_input.bam $header -o $output1 -@ \${GALAXY_SLOTS:-1}
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13 ]]>
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14 </command>
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15 <inputs>
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16 <param format="bam" label="BAM File to Convert" name="input1" type="data" />
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17 <param checked="False" falsevalue="" label="Include header in output" name="header" truevalue="-h" type="boolean" />
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18 </inputs>
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19 <outputs>
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20 <data format="sam" label="${tool.name} on ${on_string}: converted SAM" name="output1" />
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21 </outputs>
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22 <tests>
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23 <test>
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24 <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" />
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25 <param name="header" value="" />
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26 <output file="bam_to_sam_out1.sam" name="output1" sorted="True" />
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27 </test>
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28 <test>
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29 <param ftype="bam" name="input1" value="bam_to_sam_in2.bam" />
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30 <param name="header" value="" />
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31 <output file="bam_to_sam_out2.sam" name="output1" sorted="True" />
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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="True" />
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36 <output file="bam_to_sam_out3.sam" name="output1" sorted="True" />
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37 </test>
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38 </tests>
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39 <help>
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40 <![CDATA[
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41
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42 **What it does**
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43
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44 This tool uses the SAMTools_ toolkit to produce a SAM file from a BAM file.
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45
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46 .. _SAMTools: http://samtools.sourceforge.net/samtools.shtml
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47 ]]>
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48 </help>
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49 <expand macro="citations"></expand>
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50 </tool>
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