Mercurial > repos > jjohnson > mothur_toolsuite
changeset 3:b849cd7e132a
workflow cleanup_param_values recurses through paramnames whenever they start with a paramname_, so change input to input_fasta
| author | jj@dbw-galaxy-dev.msi.umn.edu |
|---|---|
| date | Wed, 08 Jun 2011 14:59:08 -0500 |
| parents | e990ac8a0f58 |
| children | 5265aa9067e0 |
| files | mothur/tools/mothur/screen.seqs.xml |
| diffstat | 1 files changed, 5 insertions(+), 5 deletions(-) [+] |
line wrap: on
line diff
--- a/mothur/tools/mothur/screen.seqs.xml Tue Jun 07 17:39:06 2011 -0400 +++ b/mothur/tools/mothur/screen.seqs.xml Wed Jun 08 14:59:08 2011 -0500 @@ -5,11 +5,11 @@ #import re, os.path --cmd='screen.seqs' #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__] - #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'\1.good.\2',$os.path.basename($input.__str__)) + ":'" + $out_file.__str__] - #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'\1.bad.accnos',$os.path.basename($input.__str__)) + ":'" + $bad_accnos.__str__] + #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'\1.good.\2',$os.path.basename($input_fasta.__str__)) + ":'" + $out_file.__str__] + #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'\1.bad.accnos',$os.path.basename($input_fasta.__str__)) + ":'" + $bad_accnos.__str__] --outputdir='$logfile.extra_files_path' --tmpdir='${logfile.extra_files_path}/input' - --fasta=$input + --fasta=$input_fasta #if int($start) >= 0: --start=$start #end if @@ -54,7 +54,7 @@ --processors=2 </command> <inputs> - <param name="input" type="data" format="fasta,align" label="fasta - Fasta to screen"/> + <param name="input_fasta" type="data" format="fasta,align" label="fasta - Fasta to screen"/> <param name="start" type="integer" value="-1" label="start - Remove sequences that start after position (ignored when negative)"/> <param name="end" type="integer" value="-1" label="end - Remove sequences that end before position (ignored when negative)"/> <param name="minlength" type="integer" value="-1" label="minlength - Remove sequences shorter than (ignored when negative)"/> @@ -77,7 +77,7 @@ </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> - <data format_source="input" name="out_file" label="${tool.name} on ${on_string}: good.${input.datatype.file_ext}" /> + <data format_source="input_fasta" name="out_file" label="${tool.name} on ${on_string}: good.${input_fasta.datatype.file_ext}" /> <data format="accnos" name="bad_accnos" label="${tool.name} on ${on_string}: bad.accnos" /> <data format_source="input_qfile" name="output_qfile" label="${tool.name} on ${on_string}: qfile" > <filter>input_qfile != None</filter>