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1 <tool id="bam_to_sqlite" name="BAM to Sqlite" version="1.8a">
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15
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2 <description>Convert BAM file to SQLITE for Trips-Viz</description>
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3 <requirements>
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4 <requirement type="package" version="0.19.0">pysam</requirement>
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5 <requirement type="package" version="1.7.0">sqlitedict</requirement>
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6 <requirement type="package" version="3.37.1">sqlite</requirement>
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7 <requirement type="package" version="1.15.1">samtools</requirement>
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8
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9 </requirements>
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10 <command>
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11 #if $refGenomeSource.genomeSource == "builtin":
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12 python $__tool_directory__/bam_to_sqlite.py $input1 ${refGenomeSource.input2_builtin.fields.path} $input3 $output1
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13 #else:
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14 python $__tool_directory__/bam_to_sqlite.py $input1 ${refGenomeSource.input2_file} $input3 $output1
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15 #end if
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16
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17 </command>
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18 <inputs>
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19 <param name="input1" type="data" format="bam" label="Sorted (samtools -n) BAM file" />
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20 <conditional name="refGenomeSource">
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21 <param name="genomeSource" type="select" label="Will you select an annotation file from your history or use a built-in option?">
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22 <option value="builtin">Use a built-in SQLITE</option>
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23 <option value="history">Use one from the history</option>
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24 </param>
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25 <when value="builtin">
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26 <param name="input2_builtin" type="select" format="sqlite" label="Select a SQLITE" help="if your organism of interest is not listed - contact RiboGalaxy team">
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27 <options from_data_table="sqlites_upd1">
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28 <filter type="sort_by" column="2" />
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29 <validator type="no_options" message="No built-ins are available" />
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30 </options>
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31 </param>
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32 </when>
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33 <when value="history">
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34 <param name="input2_file" type="data" format="sqlite" label="SQLITE File" />
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35 </when>
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36 </conditional>
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37
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38 <param name="input3" type="text" label="Description of this sample" />
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39 </inputs>
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40 <outputs>
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41 <data name="output1" format="sqlite"/>
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42 </outputs>
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43 <tests>
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44 <test>
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45 <param name="input1" value="test_n_sorted.bam" ftype="bam"/>
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46 <param name="input2" value="test_org.sqlite" ftype="sqlite"/>
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47 <param name="input3" value="TEST DESCRIPTION"/>
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48 <output name="output1" file="test_n_sorted.bamv2.sqlite" ftype="sqlite" lines_diff="4" />
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49 </test>
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50 </tests>
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51 <help>
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52 **What it does**
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53
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54 Process your transcriptome read alignments for TRIPS-Viz
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55
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56 Prerequisites:
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57 - name-sorted bam file (samtools sort -n)
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58 - TRIPS-Viz annotation file in SQLITE format.
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59 </help>
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60 <citations/>
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61 </tool>
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62
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