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1 <tool id="sam2counts_edger" name="SAM/BAM To Counts">
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2 <requirements>
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3 <requirement version="2.7">python</requirement>
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4 </requirements>
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5 <description> - Create a digital expression matrix by counting reads aligned to transcripts</description>
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6 <command interpreter="python">
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7 sam2counts_galaxy_edger.py
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8 ## Inputs.
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9 #set $gnum=1
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10 #for $group in $group_analysis
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11 --group G$gnum --treatment '${group.group}' --sample-name '${group.sample_init}'
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12 --bam-file ${group.file_init} --file-type ${group.file_init.ext}
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13 #for $input_files in $group.input_files:
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14 --group G$gnum --treatment '${group.group}' --sample-name '${input_files.sample}'
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15 --bam-file ${input_files.file} --file-type ${group.file_init.ext}
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16 #end for
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17 #set $gnum = $gnum + 1
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18 #end for
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19
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20 $use_ref
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21
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22 -o $output
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23 </command>
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24
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25 <inputs>
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26 <param name="use_ref" type="boolean" label="Files have headers?" checked="true" truevalue="" falsevalue="-r" />
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27
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28 <repeat name="group_analysis" title="Group" min="1" default="1">
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29 <param name="group" title="Group name" type="text" optional="false" label="Group name (no spaces, commas, or quotes)">
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30 <validator type="empty_field" />
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31 <validator type="regex" message="No spaces, commas, or quotes allowed">^[^\s,\'\"]+$</validator>
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32 </param>
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33 <param name="sample_init" title="Sample name" type="text" optional="false" label="Sample name (no spaces, commas, or quotes)">
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34 <validator type="empty_field" />
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35 <validator type="regex" message="No spaces, commas, or quotes allowed">^[^\s,\'\"]+$</validator>
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36 </param>
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37 <param format="sam,bam" name="file_init" type="data" label="SAM/BAM File" optional="false" help="">
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38 <validator type="empty_field" />
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39 </param>
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40 <repeat name="input_files" title="Replicate" min="1" default="1">
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41 <param name="sample" title="Sample name" type="text" optional="false" label="Sample name (no spaces, commas, or quotes)">
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42 <validator type="empty_field" />
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43 <validator type="regex" message="No spaces, commas, or quotes allowed">^[^\s,\'\"]+$</validator>
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44 </param>
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45 <param format="sam,bam" name="file" type="data" label="Add file" help=""/>
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46 </repeat>
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47 </repeat>
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48 </inputs>
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49
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50 <outputs>
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51 <data format="tabular" name="output" label="Read Counts for ${tool.name} on ${on_string}"/>
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52 </outputs>
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53
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54 <help>
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55 Sample names must be unique.
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56 </help>
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57
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58 </tool>
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