Mercurial > repos > iuc > stacks2_procrad
diff stacks_procrad.xml @ 1:ca7aa77c7f57 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
| author | iuc |
|---|---|
| date | Mon, 30 Sep 2019 14:20:50 -0400 |
| parents | 9993234400f1 |
| children | bd5ff77e2036 |
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--- a/stacks_procrad.xml Mon Jul 01 11:00:33 2019 -0400 +++ b/stacks_procrad.xml Mon Sep 30 14:20:50 2019 -0400 @@ -10,6 +10,10 @@ @FASTQ_INPUT_FUNCTIONS@ mkdir stacks_inputs stacks_outputs && +#if $output_log + ln -s '$output_log' stacks_outputs/process_radtags.stacks_inputs.log && +#end if + #set ($link_command, $inputype) = $fastq_input_nonbatch( $input_type.fqinputs, $input_type.input_type_select, "_R%d_0" ) $link_command @@ -37,9 +41,7 @@ ## Output options ## --merge not implemented in Galaxy -#if $output_log - && mv stacks_outputs/process_radtags.stacks_inputs.log $output_log -#end if + @PROCESS_FASTQ_POSTPROC@ ]]></command> @@ -107,19 +109,20 @@ <param name="options_enzyme|options_enzyme_selector" value="1"/> <param name="options_enzyme|enzyme" value="ecoRI"/> <param name="filter_cond|filter_select" value="yes"/> - <param name="filter_cond|discard" value="true"/> + <param name="filter_cond|discard" value="-q"/> <param name="filter_cond|sliding" value="0.1" /> <param name="filter_cond|score" value="11" /> <param name="filter_cond|remove" value="-c" /> - <param name="filter_cond|filter_illumina" value="--filter_illumina" /> - <param name="capture" value="true"/> + <param name="capture" value="-D"/> <param name="outype" value="gzfastq"/> + <param name="add_log" value="yes" /> + <output name="output_log" file="procrad/process_radtags2.out" lines_diff="4"/> <assert_command> <has_text text="-q" /> <has_text text="-w 0.1" /> <has_text text="-s 11" /> <has_text text="-c" /> - <has_text text="--filter_illumina" /> + <has_text text="-D" /> </assert_command> <output_collection name="demultiplexed" count="40"> <element name="PopA_01" ftype="fastqsanger.gz" md5="c7250f50138cbca747b85223aaae9565"/> @@ -147,7 +150,7 @@ <param name="options_enzyme|enzyme" value="ecoRI"/> <param name="filter_cond|filter_select" value="no"/> <param name="filter_cond|len_limit" value="50"/> - <param name="capture" value="true"/> + <param name="capture" value="-D"/> <param name="outype" value="gzfasta"/> <param name="add_log" value="yes" /> <output name="output_log" file="procrad/process_radtags_paired.out" lines_diff="4"/> @@ -195,11 +198,11 @@ <param name="options_advanced|rescue_cond|barcode_dist_1" value="2" /> <param name="options_advanced|rescue_cond|barcode_dist_2" value="2" /> <param name="options_advanced|bestrad" value="--bestrad" /> - <param name="options_advanced|retain_header" value="true"/> + <param name="options_advanced|retain_header" value="--retain_header"/> <param name="options_advanced|disable_rad_check" value="--disable_rad_check" /> - <param name="options_advanced|adapter_1" value="" /> - <param name="options_advanced|adapter_2" value="" /> - <param name="options_advanced|adapter_mm" value="" /> + <param name="options_advanced|adapter_1" value="AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA" /> + <param name="options_advanced|adapter_2" value="TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT" /> + <param name="options_advanced|adapter_mm" value="2" /> <param name="outype" value="fasta"/> <assert_command> <has_text text="-e ecoRI" /> @@ -211,6 +214,8 @@ <has_text text="--disable_rad_check" /> <has_text text="--barcode_dist_1 2" /> <has_text text="--barcode_dist_2 2" /> + <has_text text="--adapter_1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA" /> + <has_text text="--adapter_2 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT" /> <has_text text="--adapter_mm 2" /> </assert_command> <output_collection name="demultiplexed_paired" type="list:paired" count="40">