Mercurial > repos > kkonganti > cfsan_centriflaken

comparison cfsan_centriflaken.xml @ 101:ce6d9548fe89

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"planemo upload"
author kkonganti
date Thu, 04 Aug 2022 10:45:55 -0400
parents ef0b422978fd
children 4425d68a184c
comparison
equal deleted inserted replaced
100:9d9537c907bd 101:ce6d9548fe89
32 #end if 32 #end if
33 ln -sf '$pair.forward' './cpipes-input/$read_R1'; 33 ln -sf '$pair.forward' './cpipes-input/$read_R1';
34 ln -sf '$pair.reverse' './cpipes-input/$read_R2'; 34 ln -sf '$pair.reverse' './cpipes-input/$read_R2';
35 #end for 35 #end for
36 #end if 36 #end if
37 $__tool_directory__/0.3.0/cpipes 37 $__tool_directory__/0.4.0/cpipes
38 --pipeline $input_read_type_cond.pipeline_cond.pipeline 38 --pipeline $input_read_type_cond.pipeline_cond.pipeline
39 #if ($input_read_type_cond.pipeline_cond.pipeline == "centriflaken"): 39 #if ($input_read_type_cond.pipeline_cond.pipeline == "centriflaken"):
40 --fq_single_end true 40 --fq_single_end true
41 --flye_genome_size '${genome_size}' 41 --flye_genome_size '${genome_size}'
42 #if ($input_read_type_cond.pipeline_cond.long_read_platform == "nanopore_corr"): 42 #if ($input_read_type_cond.pipeline_cond.long_read_platform == "nanopore_corr"):
64 --fq_filter_by_len $fq_filter_by_len 64 --fq_filter_by_len $fq_filter_by_len
65 #end if 65 #end if
66 --fq_filename_delim '${fq_filename_delim}' 66 --fq_filename_delim '${fq_filename_delim}'
67 --fq_filename_delim_idx $fq_filename_delim_idx 67 --fq_filename_delim_idx $fq_filename_delim_idx
68 --centrifuge_extract_bug '${centrifuge_extract_bug}' 68 --centrifuge_extract_bug '${centrifuge_extract_bug}'
69 #if ($input_read_type_cond.pipeline_cond.rm_dup_seqs == "true"):
70 --seqkit_rmdup_run true
71 #end if
69 -profile kondagac; 72 -profile kondagac;
70 mv './cpipes-output/${input_read_type_cond.pipeline_cond.pipeline}-multiqc/multiqc_report.html' './multiqc_report.html' > /dev/null 2>&1 || exit 1; 73 mv './cpipes-output/${input_read_type_cond.pipeline_cond.pipeline}-multiqc/multiqc_report.html' './multiqc_report.html' > /dev/null 2>&1 || exit 1;
71 mv './cpipes-output/${input_read_type_cond.pipeline_cond.pipeline}-results/kraken2_extract_contigs' kraken2_extract_contigs > /dev/null 2>&1 || exit 1; 74 mv './cpipes-output/${input_read_type_cond.pipeline_cond.pipeline}-results/kraken2_extract_contigs' kraken2_extract_contigs > /dev/null 2>&1 || exit 1;
72 rm -rf ./cpipes-output > /dev/null 2>&1 || exit 1; 75 rm -rf ./cpipes-output > /dev/null 2>&1 || exit 1;
73 rm -rf ./work > /dev/null 2>&1 || exit 1 76 rm -rf ./work > /dev/null 2>&1 || exit 1
100 <when value="centriflaken_hy"> 103 <when value="centriflaken_hy">
101 <param name="long_read_platform" type="select" label="Mention long read sequencing platform and type" 104 <param name="long_read_platform" type="select" label="Mention long read sequencing platform and type"
102 help="THIS OPTION IS IGNORED IF THE INPUT READS ARE SHORT READS."> 105 help="THIS OPTION IS IGNORED IF THE INPUT READS ARE SHORT READS.">
103 <option value="NA" selected="true">N/A</option> 106 <option value="NA" selected="true">N/A</option>
104 </param> 107 </param>
108 <param name="rm_dup_seqs" type="select" label="Remove duplicate sequences"
109 help="Selecting yes will compare sequence content and remove identical sequences i.e. only the first occured sequence record will be saved.">
110 <option value="true">yes</option>
111 <option value="false" selected="true">no</option>
112 </param>
105 </when> 113 </when>
106 </conditional> 114 </conditional>
107 <param name="fq_suffix" value=".fastq.gz" type="text" label="Suffix of the Unpaired FASTQ"/> 115 <param name="fq_suffix" value=".fastq.gz" type="text" label="Suffix of the Unpaired FASTQ"/>
108 </when> 116 </when>
109 <when value="paired"> 117 <when value="paired">
115 </param> 123 </param>
116 <when value="centriflaken_hy"> 124 <when value="centriflaken_hy">
117 <param name="long_read_platform" type="select" label="Mention long read sequencing platform and type" 125 <param name="long_read_platform" type="select" label="Mention long read sequencing platform and type"
118 help="THIS OPTION IS IGNORED IF THE INPUT READS ARE SHORT READS."> 126 help="THIS OPTION IS IGNORED IF THE INPUT READS ARE SHORT READS.">
119 <option value="NA" selected="true">N/A</option> 127 <option value="NA" selected="true">N/A</option>
128 </param>
129 <param name="rm_dup_seqs" type="select" label="Remove duplicate sequences"
130 help="Selecting yes will compare sequence content and remove identical sequences i.e. only the first occured sequence record will be saved.">
131 <option value="true">yes</option>
132 <option value="false" selected="true">no</option>
120 </param> 133 </param>
121 </when> 134 </when>
122 </conditional> 135 </conditional>
123 <param name="fq_suffix" value="_R1_001.fastq.gz" type="text" label="Suffix of the R1 FASTQ"/> 136 <param name="fq_suffix" value="_R1_001.fastq.gz" type="text" label="Suffix of the R1 FASTQ"/>
124 <param name="fq2_suffix" value="_R2_001.fastq.gz" type="text" label="Suffix of the R2 FASTQ"/> 137 <param name="fq2_suffix" value="_R2_001.fastq.gz" type="text" label="Suffix of the R2 FASTQ"/>