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3
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1 <tool id="sam2counts" name="SAM/BAM To Counts">
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2 <description>Produce count data from SAM or BAM files</description>
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3
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4 <requirements>
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5 <requirement type="python-module">sam2counts_galaxy.py</requirement>
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6 </requirements>
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7
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8 <command interpreter="python">
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9 sam2counts_galaxy.py
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10
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11 #if str($filetype.ftype_select) == "sam":
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12 ${first_input_sam}
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13 #for $input_file_sam in $filetype.input_files_sam:
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14 ${input_file_sam.additional_input_sam}
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15 #end for
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16 #end if
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17
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18 #if str($filetype.ftype_select) == "bam":
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19 -b
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20
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21 ${first_input_bam}
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22 #for $input_file_bam in $filetype.input_files_bam:
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23 ${input_file_bam.additional_input_bam}
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24 #end for
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25 #end if
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26
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27 -o $counts
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28 -l $colnames
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29 </command>
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30
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31 <inputs>
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32 <param name="colnames" type="text" size="30" label="Short names for samples" help="A comma-separated list of short names for the samples in order">
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33 <validator type="empty_field"/>
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34 <validator type="regex" message="Must be a comma-separated tuple with no spaces">^(\w+,)+\w+$</validator>
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35 </param>
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36
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37 <conditional name="filetype">
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38
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39 <param name="ftype_select" type="select" label="Are the input files SAM or BAM format?">
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40 <option value="sam">SAM</option>
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41 <option value="bam">BAM</option>
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42 </param>
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43
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44 <when value="sam">
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45 <param format="sam" name="first_input_sam" type="data" label="SAM file" help=""/>
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46 <repeat name="input_files_sam" title="Additional SAM Files">
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47 <param format="sam" name="additional_input_sam" type="data" label="SAM file" help=""/>
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48 </repeat>
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49 </when>
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50
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51 <when value="bam">
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52 <param format="bam" name="first_input_bam" type="data" label="BAM file" help=""/>
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53 <repeat name="input_files_bam" title="Additional BAM Files">
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54 <param format="bam" name="additional_input_bam" type="data" label="BAM file" help=""/>
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55 </repeat>
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56 </when>
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57
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58 </conditional>
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59 </inputs>
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60
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61 <outputs>
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62 <data format="tabular" name="counts"/>
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63 </outputs>
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64
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65 <help>
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66 </help>
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67
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68 </tool>
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