| Previous changeset 0:ce3a667012c2 (2015-01-22) |
|
Commit message:
Uploaded |
|
added:
sam2counts_galaxy_edger.xml |
| b |
| diff -r ce3a667012c2 -r a2ef5d59bd6e sam2counts_galaxy_edger.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sam2counts_galaxy_edger.xml Thu Jan 22 03:54:56 2015 -0500 |
| [ |
| @@ -0,0 +1,58 @@ +<tool id="sam2counts_edger" name="SAM/BAM To Counts"> + <requirements> + <requirement version="2.7">python</requirement> + </requirements> + <description> - Create a digital expression matrix by counting reads aligned to transcripts</description> + <command interpreter="python"> + sam2counts_galaxy_edger.py + ## Inputs. + #set $gnum=1 + #for $group in $group_analysis + --group G$gnum --treatment '${group.group}' --sample-name '${group.sample_init}' + --bam-file ${group.file_init} --file-type ${group.file_init.ext} + #for $input_files in $group.input_files: + --group G$gnum --treatment '${group.group}' --sample-name '${input_files.sample}' + --bam-file ${input_files.file} --file-type ${group.file_init.ext} + #end for + #set $gnum = $gnum + 1 + #end for + + $use_ref + + -o $output + </command> + + <inputs> + <param name="use_ref" type="boolean" label="Files have headers?" checked="true" truevalue="" falsevalue="-r" /> + + <repeat name="group_analysis" title="Group" min="1" default="1"> + <param name="group" title="Group name" type="text" optional="false" label="Group name (no spaces, commas, or quotes)"> + <validator type="empty_field" /> + <validator type="regex" message="No spaces, commas, or quotes allowed">^[^\s,\'\"]+$</validator> + </param> + <param name="sample_init" title="Sample name" type="text" optional="false" label="Sample name (no spaces, commas, or quotes)"> + <validator type="empty_field" /> + <validator type="regex" message="No spaces, commas, or quotes allowed">^[^\s,\'\"]+$</validator> + </param> + <param format="sam,bam" name="file_init" type="data" label="SAM/BAM File" optional="false" help=""> + <validator type="empty_field" /> + </param> + <repeat name="input_files" title="Replicate" min="1" default="1"> + <param name="sample" title="Sample name" type="text" optional="false" label="Sample name (no spaces, commas, or quotes)"> + <validator type="empty_field" /> + <validator type="regex" message="No spaces, commas, or quotes allowed">^[^\s,\'\"]+$</validator> + </param> + <param format="sam,bam" name="file" type="data" label="Add file" help=""/> + </repeat> + </repeat> + </inputs> + + <outputs> + <data format="tabular" name="output" label="Read Counts for ${tool.name} on ${on_string}"/> + </outputs> + + <help> +Sample names must be unique. + </help> + +</tool> |