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annotate tools/samtools_depad/samtools_depad.xml @ 2:02572789ef6c draft

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v0.0.4 Internal changes to command line handling
author peterjc
date Tue, 16 May 2017 09:29:05 -0400
parents 01f8967ce1e0
children 588c6ce25867
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1 <tool id="samtools_depad" name="Depad SAM/BAM file" version="0.0.4">
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2 <description>samtools depad</description>
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3 <requirements>
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4 <requirement type="package" version="0.1.19">samtools</requirement>
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5 </requirements>
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6 <version_command>
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7 python $__tool_directory__/samtools_depad.py --version
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8 </version_command>
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9 <command detect_errors="aggressive">
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10 python $__tool_directory__/samtools_depad.py '$padded_ref' '$input_bam' '$input_bam.ext' '$output_bam'
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11 </command>
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12 <inputs>
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13 <param name="padded_ref" type="data" format="fasta" label="Padded FASTA file (with gap characters)" />
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14 <param name="input_bam" type="data" format="sam,bam" label="Input SAM or BAM file (mapped against the padded FASTA)" />
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15 </inputs>
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16 <outputs>
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17 <data name="output_bam" format="bam" label="$input_bam.name (depad)" />
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18 </outputs>
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19 <tests>
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20 <test>
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21 <param name="padded_ref" value="sam_spec_padded.fasta" ftype="fasta" />
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22 <param name="input_bam" value="sam_spec_padded.bam" ftype="bam" />
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23 <output name="output_bam" file="sam_spec_padded.depad.bam" ftype="bam" />
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24 </test>
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25 <test>
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26 <param name="padded_ref" value="sam_spec_padded.fasta" ftype="fasta" />
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27 <param name="input_bam" value="sam_spec_padded.sam" ftype="sam" />
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28 <output name="output_bam" file="sam_spec_padded.depad.bam" ftype="bam" />
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29 </test>
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30 </tests>
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31 <help>
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32 **What it does**
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33
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34 This tool runs the ``samtools depad`` command in the SAMtools toolkit.
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35
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36 Input is a *padded* FASTA file (with gaps represented by either ``*`` or ``-``
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37 characters) and a SAM or BAM file mapped against this *padded* FASTA file.
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38
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39 The output is a new BAM file mapped against the *unpadded* FASTA file
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40 created by removing all gap characters from the sequence.
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41
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42 **Citation**
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43
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44 If you use this Galaxy tool in work leading to a scientific publication please
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45 cite:
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46
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47 Heng Li et al (2009). The Sequence Alignment/Map format and SAMtools.
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48 Bioinformatics 25(16), 2078-9.
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49 http://dx.doi.org/10.1093/bioinformatics/btp352
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50
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51 Peter J.A. Cock (2014), Galaxy wrapper for the samtools depad command
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52 http://toolshed.g2.bx.psu.edu/view/peterjc/samtools_depad
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53
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54 This wrapper is available to install into other Galaxy Instances via the Galaxy
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55 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/samtools_depad
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56 </help>
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57 <citations>
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58 <citation type="doi">10.1093/bioinformatics/btp352</citation>
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59 </citations>
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60 </tool>