varvamp: varvamp.xml annotate

author	iuc
date	Sat, 27 Jan 2024 12:34:39 +0000
parents
children	80e18c0836e5

rev	line source
0 462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	1 <tool id="varvamp" name="varVAMP" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	2 <description>design primers for highly diverse viruses</description>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	3 <macros>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	4 <import>macros.xml</import>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	5 </macros>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	6 <xrefs>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	7 <xref type="bio.tools">varvamp</xref>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	8 </xrefs>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	9 <requirements>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	10 <requirement type="package" version="@TOOL_VERSION@">varvamp</requirement>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	11 </requirements>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	12 <version_command>varvamp --version</version_command>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	13 <command detect_errors="exit_code"><![CDATA[
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	14 VARVAMP_CONFIG=custom_config varvamp
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	15
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	16 $mode.m_select
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	17 #if $mode.main_params.specify_how in ("set_threshold", "set_both"):
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	18 --threshold $mode.main_params.threshold
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	19 #end if
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	20 #if $mode.main_params.specify_how in ("set_n_ambig", "set_both"):
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	21 --n-ambig $mode.main_params.n_ambig
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	22 #if $mode.m_select == "qpcr":
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	23 --pn-ambig $mode.main_params.pn_ambig
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	24 #end if
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	25 #end if
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	26 #if str( $mode.m_select ) == "single":
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	27 --opt-length $mode.opt_length
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	28 --max-length $mode.max_length
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	29 #if $mode.limit_report.choice == "yes":
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	30 --report-n $mode.limit_report.report_n
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	31 #end if
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	32 #elif str( $mode.m_select ) == "tiled":
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	33 --opt-length $mode.opt_length
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	34 --max-length $mode.max_length
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	35 --overlap $mode.overlap
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	36 #elif str( $mode.m_select ) == "qpcr":
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	37 --test-n $mode.test_n
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	38 --deltaG $mode.deltaG
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	39 #end if
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	40 #if $mode.filter_blast_hits.choice == "yes":
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	41 --database '${mode.filter_blast_hits.database.extra_files_path}/blastdb'
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	42 #end if
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	43 --threads \${GALAXY_SLOTS:-1}
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	44
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	45 '$alignment'
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	46 results/
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	47
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	48 #if $mode.m_select == 'qpcr' and $mode.scheme_outputs and 'primer_seqs' in $mode.scheme_outputs:
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	49 ## make the primer sequences fasta discoverable under the same name that is used in "single" mode
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	50 && mv results/oligos.fasta results/primers.fasta
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	51 #end if
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	52 #if $mode.m_select == 'tiled' and $mode.scheme_outputs and 'primer_dimers' in $mode.scheme_outputs:
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	53 ## ensure the unsolvable_primer_dimers.tsv file, which varVAMP creates only conditionally, exists in all cases, in which we try to discover it as an output
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	54 && cp -n dimers_fallback.tsv results/unsolvable_primer_dimers.tsv
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	55 #end if
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	56 ]]></command>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	57 <configfiles>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	58 <configfile filename="custom_config"><![CDATA[#if $mode.advanced_config.customize == "yes":
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	59 PRIMER_TMP = ($mode.advanced_config.basic_primer_params.PRIMER_TMP_min, $mode.advanced_config.basic_primer_params.PRIMER_TMP_max, $mode.advanced_config.basic_primer_params.PRIMER_TMP_opt)
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	60 PRIMER_GC_RANGE = ($mode.advanced_config.basic_primer_params.PRIMER_GC_RANGE_min, $mode.advanced_config.basic_primer_params.PRIMER_GC_RANGE_max, $mode.advanced_config.basic_primer_params.PRIMER_GC_RANGE_opt)
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	61 PRIMER_SIZES = ($mode.advanced_config.basic_primer_params.PRIMER_SIZES_min, $mode.advanced_config.basic_primer_params.PRIMER_SIZES_max, $mode.advanced_config.basic_primer_params.PRIMER_SIZES_opt)
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	62 PRIMER_MAX_POLYX = $mode.advanced_config.basic_primer_params.PRIMER_MAX_POLYX
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	63 PRIMER_MAX_DINUC_REPEATS = $mode.advanced_config.basic_primer_params.PRIMER_MAX_DINUC_REPEATS
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	64 PRIMER_HAIRPIN = $mode.advanced_config.basic_primer_params.PRIMER_HAIRPIN
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	65 PRIMER_GC_END = ($mode.advanced_config.basic_primer_params.PRIMER_GC_END_min, $mode.advanced_config.basic_primer_params.PRIMER_GC_END_max)
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	66 PRIMER_MIN_3_WITHOUT_AMB = $mode.advanced_config.basic_primer_params.PRIMER_MIN_3_WITHOUT_AMB
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	67 PRIMER_MAX_DIMER_TMP = $mode.advanced_config.basic_primer_params.PRIMER_MAX_DIMER_TMP
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	68 #if str($mode.m_select) == "qpcr":
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	69 QPROBE_TMP = ($mode.advanced_config.qpcr_params.QPROBE_TMP_min, $mode.advanced_config.qpcr_params.QPROBE_TMP_max, $mode.advanced_config.qpcr_params.QPROBE_TMP_opt)
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	70 QPROBE_SIZES = ($mode.advanced_config.qpcr_params.QPROBE_SIZES_min, $mode.advanced_config.qpcr_params.QPROBE_SIZES_max, $mode.advanced_config.qpcr_params.QPROBE_SIZES_opt)
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	71 QPROBE_GC_RANGE = ($mode.advanced_config.qpcr_params.QPROBE_GC_RANGE_min, $mode.advanced_config.qpcr_params.QPROBE_GC_RANGE_max, $mode.advanced_config.qpcr_params.QPROBE_GC_RANGE_opt)
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	72 QPROBE_GC_END = ($mode.advanced_config.qpcr_params.QPROBE_GC_END_min, $mode.advanced_config.qpcr_params.QPROBE_GC_END_max)
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	73 QPRIMER_DIFF = $mode.advanced_config.qpcr_params.QPRIMER_DIFF
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	74 QPROBE_TEMP_DIFF = ($mode.advanced_config.qpcr_params.QPROBE_TEMP_DIFF_min, $mode.advanced_config.qpcr_params.QPROBE_TEMP_DIFF_max)
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	75 QPROBE_DISTANCE = ($mode.advanced_config.qpcr_params.QPROBE_DISTANCE_min, $mode.advanced_config.qpcr_params.QPROBE_DISTANCE_max)
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	76 END_OVERLAP = $mode.advanced_config.qpcr_params.END_OVERLAP
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	77 QAMPLICON_LENGTH = ($mode.advanced_config.qpcr_params.QAMPLICON_LENGTH_min, $mode.advanced_config.qpcr_params.QAMPLICON_LENGTH_max)
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	78 QAMPLICON_GC = ($mode.advanced_config.qpcr_params.QAMPLICON_GC_min, $mode.advanced_config.qpcr_params.QAMPLICON_GC_max)
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	79 QAMPLICON_DEL_CUTOFF = $mode.advanced_config.qpcr_params.QAMPLICON_DEL_CUTOFF
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	80 #end if
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	81 PCR_MV_CONC = $mode.advanced_config.pcr_params.PCR_MV_CONC
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	82 PCR_DV_CONC = $mode.advanced_config.pcr_params.PCR_DV_CONC
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	83 PCR_DNTP_CONC = $mode.advanced_config.pcr_params.PCR_DNTP_CONC
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	84 PCR_DNA_CONC = $mode.advanced_config.pcr_params.PCR_DNA_CONC
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	85 PRIMER_TM_PENALTY = $mode.advanced_config.penalty_multipliers.PRIMER_TM_PENALTY
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	86 PRIMER_GC_PENALTY = $mode.advanced_config.penalty_multipliers.PRIMER_GC_PENALTY
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	87 PRIMER_SIZE_PENALTY = $mode.advanced_config.penalty_multipliers.PRIMER_SIZE_PENALTY
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	88 PRIMER_MAX_BASE_PENALTY = $mode.advanced_config.penalty_multipliers.PRIMER_MAX_BASE_PENALTY
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	89 PRIMER_3_PENALTY = $mode.advanced_config.penalty_multipliers.PRIMER_3_PENALTY
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	90 PRIMER_PERMUTATION_PENALTY = $mode.advanced_config.penalty_multipliers.PRIMER_PERMUTATION_PENALTY
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	91 #end if
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	92 #if $mode.filter_blast_hits.choice == "yes":
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	93 #if $mode.filter_blast_hits.blast_advanced_cond.blast_advanced == "yes":
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	94 BLAST_SETTINGS = {
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	95 "outfmt": "6 qseqid sseqid qlen length mismatch gapopen sstart send sstrand",
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	96 "evalue": $mode.filter_blast_hits.blast_advanced_cond.blast_params.evalue,
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	97 "reward": $mode.filter_blast_hits.blast_advanced_cond.blast_params.reward,
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	98 "penalty": $mode.filter_blast_hits.blast_advanced_cond.blast_params.penalty,
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	99 "gapopen": $mode.filter_blast_hits.blast_advanced_cond.blast_params.gapopen,
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	100 "gapextend": $mode.filter_blast_hits.blast_advanced_cond.blast_params.gapextend
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	101 }
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	102 BLAST_MAX_DIFF = $mode.filter_blast_hits.blast_advanced_cond.blast_hits_usage.BLAST_MAX_DIFF
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	103 BLAST_SIZE_MULTI = $mode.filter_blast_hits.blast_advanced_cond.blast_hits_usage.BLAST_SIZE_MULTI
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	104 BLAST_PENALTY = $mode.filter_blast_hits.blast_advanced_cond.blast_hits_usage.BLAST_PENALTY
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	105 #end if
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	106 #end if
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	107 ]]></configfile>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	108 <configfile filename="dimers_fallback.tsv"><![CDATA[#set $line = '\t'.join(['pool', 'primer_name_1', 'primer_name_2', 'dimer melting temp'])
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	109 $line]]></configfile>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	110 </configfiles>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	111 <inputs>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	112 <param name="alignment" type="data" format="fasta" label="Multiple alignment of viral sequences" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	113 <conditional name="mode">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	114 <param name="m_select" type="select" label="What kind of primers would you like to design? (varvamp mode)">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	115 <option value="single">Primers for single amplicons (single)</option>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	116 <option value="tiled">Tiled primer scheme for whole-genome sequencing (tiled)</option>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	117 <option value="qpcr">qPCR primers (qpcr)</option>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	118 </param>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	119 <when value="single">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	120 <expand macro="main_parameters" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	121 <expand macro="amplicon_length_restrictions" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	122 <expand macro="blast_options" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	123 <conditional name="limit_report">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	124 <param name="choice" type="select" label="Limit the number of amplicons to report?">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	125 <option value="no">No, report all qualifying amplicons</option>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	126 <option value="yes">Yes, set an upper limit on amplicons to be reported</option>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	127 </param>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	128 <when value="no" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	129 <when value="yes">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	130 <param argument="--report-n" type="integer" min="1" value="20" label="Report only the n highest scoring amplicons" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	131 </when>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	132 </conditional>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	133 <expand macro="customize_advanced" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	134 <expand macro="primer_scheme_outputs">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	135 <option value="amplicon_assignment">Primer-to-amplicon assignment in tabular format; lists primers belonging to the same amplicon on one line for simpler automated parsing</option>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	136 </expand>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	137 <expand macro="consensus_outputs" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	138 <expand macro="graphical_outputs" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	139 <expand macro="miscellaneous_outputs">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	140 <option value="all_primers">Binding sites of ALL high-scoring primers that were considered in BED format; includes primer penalties (lower is better) as the score column</option>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	141 </expand>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	142 </when>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	143 <when value="tiled">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	144 <expand macro="main_parameters" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	145 <expand macro="amplicon_length_restrictions" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	146 <param argument="--overlap" type="integer" min="1" value="100" label="Minimal required overlap between tiled amplicons" help="default: 100" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	147 <expand macro="blast_options" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	148 <expand macro="customize_advanced" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	149 <expand macro="primer_scheme_outputs">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	150 <option value="amplicon_assignment" selected="true">Primer-to-amplicon assignment in tabular format; lists primers belonging to the same amplicon on one line; required input for automated primer trimming in some downstream analysis workflows</option>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	151 <option value="primer_dimers" selected="true">If any primers in the tiling scheme are predicted to form primer dimers, details about these will be found in this tabular output.</option>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	152 </expand>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	153 <expand macro="consensus_outputs" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	154 <expand macro="graphical_outputs" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	155 <expand macro="miscellaneous_outputs">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	156 <option value="all_primers">Binding sites of ALL high-scoring primers that were considered in BED format; includes primer penalties (lower is better) as the score column</option>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	157 </expand>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	158 </when>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	159 <when value="qpcr">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	160 <expand macro="main_parameters">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	161 <param argument="--pn-ambig" type="integer" min="0" value="1" label="Maximum number of ambiguous nucleotides per qPCR probe to be tolerated" help="To enforce specificity of detection, varVAMP will refuse to work if you set this value higher than for the amplicon primers above, and you may actually want to set it slightly lower than that value." />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	162 </expand>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	163 <param argument="--test-n" type="integer" min="1" value="50" label="Top n qPCR amplicons to test" help="test the top n qPCR amplicons for secondary structures at the minimal primer temperature. (default: 50)" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	164 <param argument="--deltaG" type="integer" value="-3" label="Minimum free energy (kcal/mol/K) cutoff" help="Minimum free energy (kcal/mol/K) cutoff at the lowest primer melting temperature. (default: -3." />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	165 <expand macro="blast_options" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	166 <expand macro="customize_advanced">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	167 <section name="qpcr_params" title="Constraints on qPCR probes and amplicons" expanded="false">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	168 <!--basic probe parameters-->
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	169 <param name="QPROBE_TMP_min" type="integer" min="0" value="64" label="Minimal qPCR probe melting temperature" help="With varVAMP default settings, the probe melting temperatures are 7°C higher than those of amplicon primers." />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	170 <param name="QPROBE_TMP_max" type="integer" min="0" value="70" label="Maximal qPCR probe melting temperature" help="With varVAMP default settings, the probe melting temperatures are 7°C higher than those of amplicon primers." />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	171 <param name="QPROBE_TMP_opt" type="integer" min="0" value="67" label="Optimal qPCR probe melting temperature" help="With varVAMP default settings, the probe melting temperatures are 7°C higher than those of amplicon primers." />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	172 <param name="QPROBE_SIZES_min" type="integer" min="0" value="20" label="Minimal qPCR probe size" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	173 <param name="QPROBE_SIZES_max" type="integer" min="0" value="30" label="Maximal qPCR probe size" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	174 <param name="QPROBE_SIZES_opt" type="integer" min="0" value="25" label="Optimal qPCR probe size" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	175 <param name="QPROBE_GC_RANGE_min" type="integer" min="0" max="100" value="40" label="Minimal qPCR probe GC-content" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	176 <param name="QPROBE_GC_RANGE_max" type="integer" min="0" max="100" value="80" label="Maximal qPCR probe GC-content" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	177 <param name="QPROBE_GC_RANGE_opt" type="integer" min="0" max="100" value="60" label="Optimal qPCR probe GC-content" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	178 <param name="QPROBE_GC_END_min" type="integer" min="0" max="5" value="0" label="Minimal number of GCs among the 3'-terminal 5 bases of the probe" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	179 <param name="QPROBE_GC_END_max" type="integer" min="0" max="5" value="4" label="Maximal number of GCs among the 3'-terminal 5 bases of the probe" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	180 <!--constraints for amplicon design-->
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	181 <param name="QPRIMER_DIFF" type="integer" min="0" max="10" value="2" label="Maximal melting temperature difference among qPCR primers" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	182 <param name="QPROBE_TEMP_DIFF_min" type="integer" min="0" max="20" value="5" label="Minimal melting temperature difference between qPCR probe and primers" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	183 <param name="QPROBE_TEMP_DIFF_max" type="integer" min="0" max="20" value="10" label="Maximal melting temperature difference between qPCR probe and primers" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	184 <param name="QPROBE_DISTANCE_min" type="integer" min="0" max="20" value="4" label="Minimal distance of the qPCR probe from the primer on the same strand" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	185 <param name="QPROBE_DISTANCE_max" type="integer" min="0" max="20" value="15" label="Maximal distance of the qPCR probe from the primer on the same strand" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	186 <param name="END_OVERLAP" type="integer" min="0" max="10" value="5" label="End Overlap" help="Maximal overlap in bases between the ends of the qPCR probe and the primer on the opposite strand" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	187 <param name="QAMPLICON_LENGTH_min" type="integer" min="0" max="300" value="70" label="Minimal length of qPCR amplicons" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	188 <param name="QAMPLICON_LENGTH_max" type="integer" min="0" max="300" value="200" label="Maximal length of qPCR amplicons" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	189 <param name="QAMPLICON_GC_min" type="integer" min="0" max="100" value="40" label="Minimal GC-content of qPCR amplicons" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	190 <param name="QAMPLICON_GC_max" type="integer" min="0" max="100" value="60" label="Maximal GC-content of qPCR amplicons" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	191 <param name="QAMPLICON_DEL_CUTOFF" type="integer" min="0" max="10" value="4" label="Cutoff for deletions allowed in aligned regions under qPCR amplicons" help ="qPCR amplicon candidates are not considered further if they span regions of the alignment that contain deletions as long as this cutoff in bases, or longer."/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	192 </section>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	193 </expand>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	194 <expand macro="primer_scheme_outputs">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	195 <option value="qpcr_design" selected="true">qPCR amplicon details in tabular format</option>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	196 </expand>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	197 <expand macro="consensus_outputs" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	198 <expand macro="graphical_outputs" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	199 <expand macro="miscellaneous_outputs">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	200 <option value="probe_regions">List of all candidate regions of the consensus sequence that were evaluated for qPCR probes in BED format</option>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	201 </expand>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	202 </when>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	203 </conditional>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	204 </inputs>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	205 <outputs>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	206 <data name="varvamp_log" format="txt" from_work_dir="results/varvamp_log.txt" label="${tool.name} on ${on_string}: Analysis Log" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	207 <data name="primer_seqs" format="fasta" from_work_dir="results/primers.fasta" label="${tool.name} on ${on_string}: Sequences of designed oligos">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	208 <filter>mode['m_select'] in ('single', 'qpcr') and mode['scheme_outputs'] and 'primer_seqs' in mode['scheme_outputs']</filter>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	209 </data>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	210 <collection name="primer_seqs_collection" type="list" label="${tool.name} on ${on_string}: per-pool primer sequences">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	211 <filter>mode['m_select'] == 'tiled' and mode['scheme_outputs'] and 'primer_seqs' in mode['scheme_outputs']</filter>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	212 <data name="pool1_sequences" format="fasta" from_work_dir="results/primers_pool_0.fasta" label="${tool.name} on ${on_string}: Sequences of designed pool 1 primers" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	213 <data name="pool2_sequences" format="fasta" from_work_dir="results/primers_pool_1.fasta" label="${tool.name} on ${on_string}: Sequences of designed pool 2 primers" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	214 </collection>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	215 <data name="primers_bed" format="bed" from_work_dir="results/primers.bed" label="${tool.name} on ${on_string}: Primer binding sites">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	216 <filter>mode['scheme_outputs'] and 'primer_binding_sites' in mode['scheme_outputs']</filter>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	217 </data>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	218 <data name="amplicons_bed" format="bed" from_work_dir="results/amplicons.bed" label="${tool.name} on ${on_string}: Amplicon locations">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	219 <filter>mode['scheme_outputs'] and 'amplicon_sites' in mode['scheme_outputs']</filter>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	220 </data>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	221 <data name="primers_details" format="tabular" from_work_dir="results/*primers.tsv" label="${tool.name} on ${on_string}: Primer details">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	222 <filter>mode['scheme_outputs'] and 'primer_details' in mode['scheme_outputs']</filter>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	223 </data>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	224 <data name="qpcr_details" format="tabular" from_work_dir="results/qpcr_design.tsv" label="${tool.name} on ${on_string}: qPCR amplicon details" >
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	225 <filter>mode['scheme_outputs'] and 'qpcr_design' in mode['scheme_outputs']</filter>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	226 </data>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	227 <data name="primer_amplicon_assignments" format="tabular" from_work_dir="results/primer_to_amplicon_assignment.tabular" label="${tool.name} on ${on_string}: Primer to amplicon assignments">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	228 <filter>mode['scheme_outputs'] and 'amplicon_assignment' in mode['scheme_outputs']</filter>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	229 </data>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	230 <data name="unresolved_primer_dimers" format="tabular" from_work_dir="results/unsolvable_primer_dimers.tsv" label="${tool.name} on ${on_string}: Unresolved primer dimers">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	231 <filter>mode['scheme_outputs'] and 'primer_dimers' in mode['scheme_outputs']</filter>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	232 </data>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	233 <data name="ambiguous_consensus" format="fasta" from_work_dir="results/ambiguous_consensus.fasta" label="${tool.name} on ${on_string}: Ambiguous consensus sequence">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	234 <filter>mode['aln_cons_outputs'] and 'ambiguous_consensus' in mode['aln_cons_outputs']</filter>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	235 </data>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	236 <data name="majority_consensus" format="fasta" from_work_dir="results/data/majority_consensus.fasta" label="${tool.name} on ${on_string}: Majority consensus sequence (no ambiguity codes)">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	237 <filter>mode['aln_cons_outputs'] and 'majority_consensus' in mode['aln_cons_outputs']</filter>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	238 </data>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	239 <data name="alignment_cleaned" format="fasta" from_work_dir="results/data/alignment_cleaned.fasta" label="${tool.name} on ${on_string}: Alignment cleaned">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	240 <filter>mode['aln_cons_outputs'] and 'alignment_cleaned' in mode['aln_cons_outputs']</filter>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	241 </data>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	242 <data name="amplicon_plot" format="pdf" from_work_dir="results/amplicon_plot.pdf" label="${tool.name} on ${on_string}: Amplicon design overview plot">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	243 <filter>mode['plot_outputs'] and 'amplicon_plot' in mode['plot_outputs']</filter>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	244 </data>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	245 <data name="per_base_mismatches" format="pdf" from_work_dir="results/per_base_mismatches.pdf" label="${tool.name} on ${on_string}: Per-base mismatches barplots">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	246 <filter>mode['plot_outputs'] and 'per_base_mismatches' in mode['plot_outputs']</filter>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	247 </data>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	248 <data name="primer_regions" format="bed" from_work_dir="results/data/primer_regions.bed" label="${tool.name} on ${on_string}: All candidate primer regions">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	249 <filter>mode['misc_outputs'] and 'primer_regions' in mode['misc_outputs']</filter>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	250 </data>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	251 <data name="probe_regions" format="bed" from_work_dir="results/data/probe_regions.bed" label="${tool.name} on ${on_string}: All candidate qPCR probe regions">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	252 <filter>mode['misc_outputs'] and 'probe_regions' in mode['misc_outputs']</filter>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	253 </data>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	254 <data name="all_primers" format="bed" from_work_dir="results/data/all_primers.bed" label="${tool.name} on ${on_string}: All primer sites">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	255 <filter>mode['misc_outputs'] and 'all_primers' in mode['misc_outputs']</filter>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	256 </data>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	257 </outputs>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	258 <tests>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	259 <test expect_num_outputs="8">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	260 <param name="alignment" value="hepatitis_e_aln_shrunk.fasta"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	261 <conditional name="mode">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	262 <param name='m_select' value="single"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	263 <conditional name="main_params">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	264 <param name="specify_how" value="set_both"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	265 <param name="threshold" value="0.8"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	266 <param name="n_ambig" value="3"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	267 </conditional>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	268 <param name="opt_length" value="300"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	269 <param name="max_length" value="400"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	270 <conditional name="limit_report">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	271 <param name="choice" value="yes" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	272 <param name="report_n" value="5"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	273 </conditional>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	274 </conditional>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	275 <output name="varvamp_log" ftype="txt" compare="contains" file="test1.log" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	276 <output name="ambiguous_consensus" ftype="fasta" file="ambiguous_consensus.fasta" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	277 <output name="amplicon_plot" ftype="pdf">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	278 <assert_contents>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	279 <has_text text="%PDF"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	280 <has_text text="%%EOF"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	281 </assert_contents>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	282 </output>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	283 <output name="primers_bed" ftype="bed">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	284 <assert_contents>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	285 <has_n_lines n="2" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	286 </assert_contents>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	287 </output>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	288 <output name="amplicons_bed" ftype="bed">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	289 <assert_contents>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	290 <has_n_lines n="1"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	291 </assert_contents>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	292 </output>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	293 <output name="per_base_mismatches" ftype="pdf">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	294 <assert_contents>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	295 <has_text text="%PDF"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	296 <has_text text="%%EOF"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	297 </assert_contents>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	298 </output>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	299 <output name="primer_seqs" ftype="fasta">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	300 <assert_contents>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	301 <has_line line=">AMPLICON_0_LEFT"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	302 <has_line line=">AMPLICON_0_RIGHT"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	303 <has_n_lines n="4"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	304 </assert_contents>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	305 </output>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	306 </test>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	307 <test expect_num_outputs="12">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	308 <param name="alignment" value="hepatitis_e_aln_shrunk.fasta"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	309 <conditional name="mode">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	310 <param name='m_select' value="tiled"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	311 <conditional name="main_params">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	312 <param name="specify_how" value="set_both"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	313 <param name="threshold" value="0.6"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	314 <param name="n_ambig" value="2"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	315 </conditional>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	316 <param name="opt_length" value="150"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	317 <param name="max_length" value="300"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	318 <param name="overlap" value="100"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	319 </conditional>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	320 <output name="varvamp_log" ftype="txt" compare="contains" file="test2.log" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	321 <output name="primers_bed" ftype="bed">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	322 <assert_contents>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	323 <has_n_lines n="4" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	324 </assert_contents>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	325 </output>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	326 <output name="amplicons_bed" ftype="bed">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	327 <assert_contents>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	328 <has_n_lines n="2"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	329 </assert_contents>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	330 </output>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	331 <output name="primer_amplicon_assignments" ftype="tabular">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	332 <assert_contents>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	333 <has_n_lines n="2"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	334 <has_n_columns n="2"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	335 </assert_contents>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	336 </output>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	337 <output name="unresolved_primer_dimers" ftype="tabular">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	338 <assert_contents>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	339 <has_n_lines n="1"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	340 </assert_contents>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	341 </output>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	342 <output_collection name="primer_seqs_collection" type="list" count="2">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	343 <element name="pool1_sequences" ftype="fasta">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	344 <assert_contents>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	345 <has_n_lines n="4"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	346 <has_line line=">AMPLICON_0_LEFT"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	347 </assert_contents>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	348 </element>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	349 <element name="pool2_sequences" ftype="fasta">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	350 <assert_contents>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	351 <has_n_lines n="4"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	352 <has_line line=">AMPLICON_1_LEFT"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	353 </assert_contents>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	354 </element>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	355 </output_collection>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	356 </test>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	357 <test expect_num_outputs="9">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	358 <param name="alignment" value="hepatitis_e_aln_shrunk.fasta"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	359 <conditional name="mode">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	360 <param name='m_select' value="qpcr"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	361 <conditional name="main_params">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	362 <param name="specify_how" value="set_both"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	363 <param name="threshold" value="0.7"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	364 <param name="n_ambig" value="1"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	365 <param name="pn_ambig" value="1"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	366 </conditional>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	367 <param name="test_n" value="180"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	368 <param name="deltaG" value="-15"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	369 </conditional>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	370 <output name="varvamp_log" ftype="txt" compare="contains" file="test3.log" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	371 <output name="primers_bed" ftype="bed">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	372 <assert_contents>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	373 <has_n_lines n="3" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	374 </assert_contents>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	375 </output>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	376 <output name="amplicons_bed" ftype="bed">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	377 <assert_contents>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	378 <has_n_lines n="1"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	379 </assert_contents>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	380 </output>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	381 <output name="primer_seqs" ftype="fasta">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	382 <assert_contents>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	383 <has_line line=">QPCR_SCHEME_0_PROBE"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	384 <has_line line=">QPCR_SCHEME_0_LEFT"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	385 <has_line line=">QPCR_SCHEME_0_RIGHT"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	386 <has_n_lines n="6"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	387 </assert_contents>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	388 </output>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	389 <output name="qpcr_details" ftype="tabular">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	390 <assert_contents>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	391 <has_n_lines n="2"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	392 </assert_contents>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	393 </output>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	394 </test>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	395 <test expect_num_outputs="1">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	396 <!-- Similar to test 1, but try to modify some of varVAMP's
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	397 advanced params, and see whether that gets reflected in the log file.
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	398 -->
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	399 <param name="alignment" value="hepatitis_e_aln_shrunk.fasta"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	400 <conditional name="mode">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	401 <param name='m_select' value="single"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	402 <conditional name="main_params">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	403 <param name="specify_how" value="set_both"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	404 <param name="threshold" value="0.8"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	405 <param name="n_ambig" value="3"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	406 </conditional>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	407 <param name="opt_length" value="300"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	408 <param name="max_length" value="400"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	409 <conditional name="limit_report">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	410 <param name="choice" value="yes" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	411 <param name="report_n" value="5"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	412 </conditional>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	413 <conditional name="advanced_config">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	414 <param name="customize" value="yes"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	415 <section name="basic_primer_params">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	416 <param name="PRIMER_GC_RANGE_min" value="20"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	417 <param name="PRIMER_GC_RANGE_max" value="80"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	418 </section>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	419 </conditional>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	420 <param name="scheme_outputs" value=""/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	421 <param name="aln_cons_outputs" value=""/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	422 <param name="plot_outputs" value=""/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	423 <param name="misc_outputs" value=""/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	424 </conditional>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	425 <output name="varvamp_log" ftype="txt" compare="contains" file="test4.log" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	426 </test>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	427 </tests>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	428 <help><![CDATA[
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	429
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	430 .. class:: infomark
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	431
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	432 What it does
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	433
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	434 variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences.
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	435
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	436 For a lot of virus genera it is difficult to design pan-specific primers. varVAMP solves this by introducing ambiguous characters into primers and minimizes mismatches at the 3' end. Primers might not work for some sequences of your input alignment but should recognize the large majority.
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	437
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	438 varVAMP can be run in three different modes:
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	439
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	440 * SINGLE: varVAMP searches for the very best primers and reports back non-overlapping amplicons which can be used for PCR-based screening approaches.
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	441 * TILED: varVAMP uses a graph based approach to design overlapping (tiled) amplicons that together cover the entire viral genome. This designs amplicons that are suitable for Oxford Nanopore or Illumina based full-genome sequencing.
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	442 * QPCR: varVAMP searches for small amplicons with an optimized internal probe (TaqMan). It minimizes temperature differences between the primers and checks for amplicon secondary structures.
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	443
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	444 Algorithmic parameters:
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	445
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	446 These are explained very well on the `How varVAMP works <https://github.com/jonas-fuchs/varVAMP/blob/master/docs/how_varvamp_works.md>`__ page of the varVAMP documentation.
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	447
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	448 Outputs:
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	449
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	450 This tool can produce lots of informative output and the different modes come with what we hope are reasonable default choices.
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	451
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	452 The most important output, however, is the Analysis Log, which will always be generated and contains essential information about what parameters where used by varVAMP during the run and about intermediate results. You should always check this file. Together with the tool's standard output and error streams, it is the place to spot issues with your analysis and to start debugging them.
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	453
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	454 .. class:: infomark
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	455
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	456 Testing with a new alignment/analysis:
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	457
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	458 As a first check whether a new alignment of viral sequences can be used with specific settings of the tool, it may help to disable all configurable outputs, which will leave you with only the Analysis Log. This will be enough to see if there are any errors with the combination of alignment and settings, and whether you are on a roughly correct track (varVAMP reports some primers, for example). This way, you're not flooding your analysis history with lots of likely useless datasets, and once you've fixed potential issues you can add back more outputs and rerun the analysis.
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	459 ]]></help>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	460 <citations>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	461 <citation type="doi">https://github.com/jonas-fuchs/varVAMP/</citation>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	462 </citations>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	463 </tool>

0

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

1 <tool id="varvamp" name="varVAMP" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

2 <description>design primers for highly diverse viruses</description>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

3 <macros>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

4 <import>macros.xml</import>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

5 </macros>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

6 <xrefs>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

7 <xref type="bio.tools">varvamp</xref>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

8 </xrefs>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

9 <requirements>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

10 <requirement type="package" version="@TOOL_VERSION@">varvamp</requirement>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

11 </requirements>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

12 <version_command>varvamp --version</version_command>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

13 <command detect_errors="exit_code"><![CDATA[

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

14 VARVAMP_CONFIG=custom_config varvamp

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

15

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

16 $mode.m_select

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

17 #if $mode.main_params.specify_how in ("set_threshold", "set_both"):

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

18 --threshold $mode.main_params.threshold

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

19 #end if

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

20 #if $mode.main_params.specify_how in ("set_n_ambig", "set_both"):

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

21 --n-ambig $mode.main_params.n_ambig

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

22 #if $mode.m_select == "qpcr":

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

23 --pn-ambig $mode.main_params.pn_ambig

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

24 #end if

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

25 #end if

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

26 #if str( $mode.m_select ) == "single":

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

27 --opt-length $mode.opt_length

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

28 --max-length $mode.max_length

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

29 #if $mode.limit_report.choice == "yes":

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

30 --report-n $mode.limit_report.report_n

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

31 #end if

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

32 #elif str( $mode.m_select ) == "tiled":

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

33 --opt-length $mode.opt_length

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

34 --max-length $mode.max_length

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

35 --overlap $mode.overlap

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

36 #elif str( $mode.m_select ) == "qpcr":

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

37 --test-n $mode.test_n

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

38 --deltaG $mode.deltaG

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

39 #end if

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

40 #if $mode.filter_blast_hits.choice == "yes":

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

41 --database '${mode.filter_blast_hits.database.extra_files_path}/blastdb'

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

42 #end if

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

43 --threads \${GALAXY_SLOTS:-1}

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

44

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

45 '$alignment'

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

46 results/

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

47

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

48 #if $mode.m_select == 'qpcr' and $mode.scheme_outputs and 'primer_seqs' in $mode.scheme_outputs:

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

49 ## make the primer sequences fasta discoverable under the same name that is used in "single" mode

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

50 && mv results/oligos.fasta results/primers.fasta

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

51 #end if

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

52 #if $mode.m_select == 'tiled' and $mode.scheme_outputs and 'primer_dimers' in $mode.scheme_outputs:

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

53 ## ensure the unsolvable_primer_dimers.tsv file, which varVAMP creates only conditionally, exists in all cases, in which we try to discover it as an output

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

54 && cp -n dimers_fallback.tsv results/unsolvable_primer_dimers.tsv

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

55 #end if

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

56 ]]></command>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

57 <configfiles>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

58 <configfile filename="custom_config"><![CDATA[#if $mode.advanced_config.customize == "yes":

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

59 PRIMER_TMP = ($mode.advanced_config.basic_primer_params.PRIMER_TMP_min, $mode.advanced_config.basic_primer_params.PRIMER_TMP_max, $mode.advanced_config.basic_primer_params.PRIMER_TMP_opt)

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

60 PRIMER_GC_RANGE = ($mode.advanced_config.basic_primer_params.PRIMER_GC_RANGE_min, $mode.advanced_config.basic_primer_params.PRIMER_GC_RANGE_max, $mode.advanced_config.basic_primer_params.PRIMER_GC_RANGE_opt)

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

61 PRIMER_SIZES = ($mode.advanced_config.basic_primer_params.PRIMER_SIZES_min, $mode.advanced_config.basic_primer_params.PRIMER_SIZES_max, $mode.advanced_config.basic_primer_params.PRIMER_SIZES_opt)

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

62 PRIMER_MAX_POLYX = $mode.advanced_config.basic_primer_params.PRIMER_MAX_POLYX

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

63 PRIMER_MAX_DINUC_REPEATS = $mode.advanced_config.basic_primer_params.PRIMER_MAX_DINUC_REPEATS

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

64 PRIMER_HAIRPIN = $mode.advanced_config.basic_primer_params.PRIMER_HAIRPIN

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

65 PRIMER_GC_END = ($mode.advanced_config.basic_primer_params.PRIMER_GC_END_min, $mode.advanced_config.basic_primer_params.PRIMER_GC_END_max)

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

66 PRIMER_MIN_3_WITHOUT_AMB = $mode.advanced_config.basic_primer_params.PRIMER_MIN_3_WITHOUT_AMB

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

67 PRIMER_MAX_DIMER_TMP = $mode.advanced_config.basic_primer_params.PRIMER_MAX_DIMER_TMP

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

68 #if str($mode.m_select) == "qpcr":

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

69 QPROBE_TMP = ($mode.advanced_config.qpcr_params.QPROBE_TMP_min, $mode.advanced_config.qpcr_params.QPROBE_TMP_max, $mode.advanced_config.qpcr_params.QPROBE_TMP_opt)

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

70 QPROBE_SIZES = ($mode.advanced_config.qpcr_params.QPROBE_SIZES_min, $mode.advanced_config.qpcr_params.QPROBE_SIZES_max, $mode.advanced_config.qpcr_params.QPROBE_SIZES_opt)

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

71 QPROBE_GC_RANGE = ($mode.advanced_config.qpcr_params.QPROBE_GC_RANGE_min, $mode.advanced_config.qpcr_params.QPROBE_GC_RANGE_max, $mode.advanced_config.qpcr_params.QPROBE_GC_RANGE_opt)

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

72 QPROBE_GC_END = ($mode.advanced_config.qpcr_params.QPROBE_GC_END_min, $mode.advanced_config.qpcr_params.QPROBE_GC_END_max)

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

73 QPRIMER_DIFF = $mode.advanced_config.qpcr_params.QPRIMER_DIFF

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

74 QPROBE_TEMP_DIFF = ($mode.advanced_config.qpcr_params.QPROBE_TEMP_DIFF_min, $mode.advanced_config.qpcr_params.QPROBE_TEMP_DIFF_max)

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

75 QPROBE_DISTANCE = ($mode.advanced_config.qpcr_params.QPROBE_DISTANCE_min, $mode.advanced_config.qpcr_params.QPROBE_DISTANCE_max)

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

76 END_OVERLAP = $mode.advanced_config.qpcr_params.END_OVERLAP

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

77 QAMPLICON_LENGTH = ($mode.advanced_config.qpcr_params.QAMPLICON_LENGTH_min, $mode.advanced_config.qpcr_params.QAMPLICON_LENGTH_max)

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

78 QAMPLICON_GC = ($mode.advanced_config.qpcr_params.QAMPLICON_GC_min, $mode.advanced_config.qpcr_params.QAMPLICON_GC_max)

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

79 QAMPLICON_DEL_CUTOFF = $mode.advanced_config.qpcr_params.QAMPLICON_DEL_CUTOFF

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

80 #end if

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

81 PCR_MV_CONC = $mode.advanced_config.pcr_params.PCR_MV_CONC

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

82 PCR_DV_CONC = $mode.advanced_config.pcr_params.PCR_DV_CONC

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

83 PCR_DNTP_CONC = $mode.advanced_config.pcr_params.PCR_DNTP_CONC

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

84 PCR_DNA_CONC = $mode.advanced_config.pcr_params.PCR_DNA_CONC

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

85 PRIMER_TM_PENALTY = $mode.advanced_config.penalty_multipliers.PRIMER_TM_PENALTY

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

86 PRIMER_GC_PENALTY = $mode.advanced_config.penalty_multipliers.PRIMER_GC_PENALTY

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

87 PRIMER_SIZE_PENALTY = $mode.advanced_config.penalty_multipliers.PRIMER_SIZE_PENALTY

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

88 PRIMER_MAX_BASE_PENALTY = $mode.advanced_config.penalty_multipliers.PRIMER_MAX_BASE_PENALTY

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

89 PRIMER_3_PENALTY = $mode.advanced_config.penalty_multipliers.PRIMER_3_PENALTY

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

90 PRIMER_PERMUTATION_PENALTY = $mode.advanced_config.penalty_multipliers.PRIMER_PERMUTATION_PENALTY

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

91 #end if

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

92 #if $mode.filter_blast_hits.choice == "yes":

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

93 #if $mode.filter_blast_hits.blast_advanced_cond.blast_advanced == "yes":

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

94 BLAST_SETTINGS = {

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

95 "outfmt": "6 qseqid sseqid qlen length mismatch gapopen sstart send sstrand",

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

96 "evalue": $mode.filter_blast_hits.blast_advanced_cond.blast_params.evalue,

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

97 "reward": $mode.filter_blast_hits.blast_advanced_cond.blast_params.reward,

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

98 "penalty": $mode.filter_blast_hits.blast_advanced_cond.blast_params.penalty,

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

99 "gapopen": $mode.filter_blast_hits.blast_advanced_cond.blast_params.gapopen,

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

100 "gapextend": $mode.filter_blast_hits.blast_advanced_cond.blast_params.gapextend

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

101 }

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

102 BLAST_MAX_DIFF = $mode.filter_blast_hits.blast_advanced_cond.blast_hits_usage.BLAST_MAX_DIFF

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

103 BLAST_SIZE_MULTI = $mode.filter_blast_hits.blast_advanced_cond.blast_hits_usage.BLAST_SIZE_MULTI

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

104 BLAST_PENALTY = $mode.filter_blast_hits.blast_advanced_cond.blast_hits_usage.BLAST_PENALTY

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

105 #end if

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

106 #end if

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

107 ]]></configfile>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

108 <configfile filename="dimers_fallback.tsv"><![CDATA[#set $line = '\t'.join(['pool', 'primer_name_1', 'primer_name_2', 'dimer melting temp'])

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

109 $line]]></configfile>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

110 </configfiles>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

111 <inputs>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

112 <param name="alignment" type="data" format="fasta" label="Multiple alignment of viral sequences" />

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

113 <conditional name="mode">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

114 <param name="m_select" type="select" label="What kind of primers would you like to design? (varvamp mode)">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

115 <option value="single">Primers for single amplicons (single)</option>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

116 <option value="tiled">Tiled primer scheme for whole-genome sequencing (tiled)</option>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

117 <option value="qpcr">qPCR primers (qpcr)</option>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

118 </param>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

119 <when value="single">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

120 <expand macro="main_parameters" />

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

121 <expand macro="amplicon_length_restrictions" />

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

122 <expand macro="blast_options" />

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

123 <conditional name="limit_report">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

124 <param name="choice" type="select" label="Limit the number of amplicons to report?">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

125 <option value="no">No, report all qualifying amplicons</option>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

126 <option value="yes">Yes, set an upper limit on amplicons to be reported</option>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

127 </param>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

128 <when value="no" />

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

129 <when value="yes">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

130 <param argument="--report-n" type="integer" min="1" value="20" label="Report only the n highest scoring amplicons" />

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

131 </when>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

132 </conditional>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

133 <expand macro="customize_advanced" />

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

134 <expand macro="primer_scheme_outputs">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

135 <option value="amplicon_assignment">Primer-to-amplicon assignment in tabular format; lists primers belonging to the same amplicon on one line for simpler automated parsing</option>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

136 </expand>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

137 <expand macro="consensus_outputs" />

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

138 <expand macro="graphical_outputs" />

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

139 <expand macro="miscellaneous_outputs">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

140 <option value="all_primers">Binding sites of ALL high-scoring primers that were considered in BED format; includes primer penalties (lower is better) as the score column</option>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

141 </expand>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

142 </when>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

143 <when value="tiled">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

144 <expand macro="main_parameters" />

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

145 <expand macro="amplicon_length_restrictions" />

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

146 <param argument="--overlap" type="integer" min="1" value="100" label="Minimal required overlap between tiled amplicons" help="default: 100" />

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

147 <expand macro="blast_options" />

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

148 <expand macro="customize_advanced" />

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

149 <expand macro="primer_scheme_outputs">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

150 <option value="amplicon_assignment" selected="true">Primer-to-amplicon assignment in tabular format; lists primers belonging to the same amplicon on one line; required input for automated primer trimming in some downstream analysis workflows</option>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

151 <option value="primer_dimers" selected="true">If any primers in the tiling scheme are predicted to form primer dimers, details about these will be found in this tabular output.</option>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

152 </expand>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

153 <expand macro="consensus_outputs" />

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

154 <expand macro="graphical_outputs" />

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

155 <expand macro="miscellaneous_outputs">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

156 <option value="all_primers">Binding sites of ALL high-scoring primers that were considered in BED format; includes primer penalties (lower is better) as the score column</option>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

157 </expand>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

158 </when>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

159 <when value="qpcr">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

160 <expand macro="main_parameters">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

161 <param argument="--pn-ambig" type="integer" min="0" value="1" label="Maximum number of ambiguous nucleotides per qPCR probe to be tolerated" help="To enforce specificity of detection, varVAMP will refuse to work if you set this value higher than for the amplicon primers above, and you may actually want to set it slightly lower than that value." />

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

162 </expand>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

163 <param argument="--test-n" type="integer" min="1" value="50" label="Top n qPCR amplicons to test" help="test the top n qPCR amplicons for secondary structures at the minimal primer temperature. (default: 50)" />

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

164 <param argument="--deltaG" type="integer" value="-3" label="Minimum free energy (kcal/mol/K) cutoff" help="Minimum free energy (kcal/mol/K) cutoff at the lowest primer melting temperature. (default: -3." />

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

165 <expand macro="blast_options" />

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

166 <expand macro="customize_advanced">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

167 <section name="qpcr_params" title="Constraints on qPCR probes and amplicons" expanded="false">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

168

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

169 <param name="QPROBE_TMP_min" type="integer" min="0" value="64" label="Minimal qPCR probe melting temperature" help="With varVAMP default settings, the probe melting temperatures are 7°C higher than those of amplicon primers." />

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

170 <param name="QPROBE_TMP_max" type="integer" min="0" value="70" label="Maximal qPCR probe melting temperature" help="With varVAMP default settings, the probe melting temperatures are 7°C higher than those of amplicon primers." />

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

171 <param name="QPROBE_TMP_opt" type="integer" min="0" value="67" label="Optimal qPCR probe melting temperature" help="With varVAMP default settings, the probe melting temperatures are 7°C higher than those of amplicon primers." />

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

172 <param name="QPROBE_SIZES_min" type="integer" min="0" value="20" label="Minimal qPCR probe size" />

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

173 <param name="QPROBE_SIZES_max" type="integer" min="0" value="30" label="Maximal qPCR probe size" />

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

174 <param name="QPROBE_SIZES_opt" type="integer" min="0" value="25" label="Optimal qPCR probe size" />

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

175 <param name="QPROBE_GC_RANGE_min" type="integer" min="0" max="100" value="40" label="Minimal qPCR probe GC-content" />

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

176 <param name="QPROBE_GC_RANGE_max" type="integer" min="0" max="100" value="80" label="Maximal qPCR probe GC-content" />

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

177 <param name="QPROBE_GC_RANGE_opt" type="integer" min="0" max="100" value="60" label="Optimal qPCR probe GC-content" />

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

178 <param name="QPROBE_GC_END_min" type="integer" min="0" max="5" value="0" label="Minimal number of GCs among the 3'-terminal 5 bases of the probe" />

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

179 <param name="QPROBE_GC_END_max" type="integer" min="0" max="5" value="4" label="Maximal number of GCs among the 3'-terminal 5 bases of the probe" />

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

180

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

181 <param name="QPRIMER_DIFF" type="integer" min="0" max="10" value="2" label="Maximal melting temperature difference among qPCR primers" />

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

182 <param name="QPROBE_TEMP_DIFF_min" type="integer" min="0" max="20" value="5" label="Minimal melting temperature difference between qPCR probe and primers" />

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

183 <param name="QPROBE_TEMP_DIFF_max" type="integer" min="0" max="20" value="10" label="Maximal melting temperature difference between qPCR probe and primers" />

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

184 <param name="QPROBE_DISTANCE_min" type="integer" min="0" max="20" value="4" label="Minimal distance of the qPCR probe from the primer on the same strand" />

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

185 <param name="QPROBE_DISTANCE_max" type="integer" min="0" max="20" value="15" label="Maximal distance of the qPCR probe from the primer on the same strand" />

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

186 <param name="END_OVERLAP" type="integer" min="0" max="10" value="5" label="End Overlap" help="Maximal overlap in bases between the ends of the qPCR probe and the primer on the opposite strand" />

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

187 <param name="QAMPLICON_LENGTH_min" type="integer" min="0" max="300" value="70" label="Minimal length of qPCR amplicons" />

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

188 <param name="QAMPLICON_LENGTH_max" type="integer" min="0" max="300" value="200" label="Maximal length of qPCR amplicons" />

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

189 <param name="QAMPLICON_GC_min" type="integer" min="0" max="100" value="40" label="Minimal GC-content of qPCR amplicons" />

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

190 <param name="QAMPLICON_GC_max" type="integer" min="0" max="100" value="60" label="Maximal GC-content of qPCR amplicons" />

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

191 <param name="QAMPLICON_DEL_CUTOFF" type="integer" min="0" max="10" value="4" label="Cutoff for deletions allowed in aligned regions under qPCR amplicons" help ="qPCR amplicon candidates are not considered further if they span regions of the alignment that contain deletions as long as this cutoff in bases, or longer."/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

192 </section>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

193 </expand>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

194 <expand macro="primer_scheme_outputs">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

195 <option value="qpcr_design" selected="true">qPCR amplicon details in tabular format</option>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

196 </expand>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

197 <expand macro="consensus_outputs" />

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

198 <expand macro="graphical_outputs" />

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

199 <expand macro="miscellaneous_outputs">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

200 <option value="probe_regions">List of all candidate regions of the consensus sequence that were evaluated for qPCR probes in BED format</option>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

201 </expand>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

202 </when>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

203 </conditional>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

204 </inputs>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

205 <outputs>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

206 <data name="varvamp_log" format="txt" from_work_dir="results/varvamp_log.txt" label="${tool.name} on ${on_string}: Analysis Log" />

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

207 <data name="primer_seqs" format="fasta" from_work_dir="results/primers.fasta" label="${tool.name} on ${on_string}: Sequences of designed oligos">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

208 <filter>mode['m_select'] in ('single', 'qpcr') and mode['scheme_outputs'] and 'primer_seqs' in mode['scheme_outputs']</filter>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

209 </data>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

210 <collection name="primer_seqs_collection" type="list" label="${tool.name} on ${on_string}: per-pool primer sequences">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

211 <filter>mode['m_select'] == 'tiled' and mode['scheme_outputs'] and 'primer_seqs' in mode['scheme_outputs']</filter>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

212 <data name="pool1_sequences" format="fasta" from_work_dir="results/primers_pool_0.fasta" label="${tool.name} on ${on_string}: Sequences of designed pool 1 primers" />

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

213 <data name="pool2_sequences" format="fasta" from_work_dir="results/primers_pool_1.fasta" label="${tool.name} on ${on_string}: Sequences of designed pool 2 primers" />

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

214 </collection>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

215 <data name="primers_bed" format="bed" from_work_dir="results/primers.bed" label="${tool.name} on ${on_string}: Primer binding sites">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

216 <filter>mode['scheme_outputs'] and 'primer_binding_sites' in mode['scheme_outputs']</filter>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

217 </data>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

218 <data name="amplicons_bed" format="bed" from_work_dir="results/amplicons.bed" label="${tool.name} on ${on_string}: Amplicon locations">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

219 <filter>mode['scheme_outputs'] and 'amplicon_sites' in mode['scheme_outputs']</filter>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

220 </data>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

221 <data name="primers_details" format="tabular" from_work_dir="results/*primers.tsv" label="${tool.name} on ${on_string}: Primer details">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

222 <filter>mode['scheme_outputs'] and 'primer_details' in mode['scheme_outputs']</filter>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

223 </data>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

224 <data name="qpcr_details" format="tabular" from_work_dir="results/qpcr_design.tsv" label="${tool.name} on ${on_string}: qPCR amplicon details" >

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

225 <filter>mode['scheme_outputs'] and 'qpcr_design' in mode['scheme_outputs']</filter>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

226 </data>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

227 <data name="primer_amplicon_assignments" format="tabular" from_work_dir="results/primer_to_amplicon_assignment.tabular" label="${tool.name} on ${on_string}: Primer to amplicon assignments">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

228 <filter>mode['scheme_outputs'] and 'amplicon_assignment' in mode['scheme_outputs']</filter>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

229 </data>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

230 <data name="unresolved_primer_dimers" format="tabular" from_work_dir="results/unsolvable_primer_dimers.tsv" label="${tool.name} on ${on_string}: Unresolved primer dimers">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

231 <filter>mode['scheme_outputs'] and 'primer_dimers' in mode['scheme_outputs']</filter>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

232 </data>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

233 <data name="ambiguous_consensus" format="fasta" from_work_dir="results/ambiguous_consensus.fasta" label="${tool.name} on ${on_string}: Ambiguous consensus sequence">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

234 <filter>mode['aln_cons_outputs'] and 'ambiguous_consensus' in mode['aln_cons_outputs']</filter>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

235 </data>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

236 <data name="majority_consensus" format="fasta" from_work_dir="results/data/majority_consensus.fasta" label="${tool.name} on ${on_string}: Majority consensus sequence (no ambiguity codes)">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

237 <filter>mode['aln_cons_outputs'] and 'majority_consensus' in mode['aln_cons_outputs']</filter>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

238 </data>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

239 <data name="alignment_cleaned" format="fasta" from_work_dir="results/data/alignment_cleaned.fasta" label="${tool.name} on ${on_string}: Alignment cleaned">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

240 <filter>mode['aln_cons_outputs'] and 'alignment_cleaned' in mode['aln_cons_outputs']</filter>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

241 </data>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

242 <data name="amplicon_plot" format="pdf" from_work_dir="results/amplicon_plot.pdf" label="${tool.name} on ${on_string}: Amplicon design overview plot">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

243 <filter>mode['plot_outputs'] and 'amplicon_plot' in mode['plot_outputs']</filter>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

244 </data>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

245 <data name="per_base_mismatches" format="pdf" from_work_dir="results/per_base_mismatches.pdf" label="${tool.name} on ${on_string}: Per-base mismatches barplots">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

246 <filter>mode['plot_outputs'] and 'per_base_mismatches' in mode['plot_outputs']</filter>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

247 </data>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

248 <data name="primer_regions" format="bed" from_work_dir="results/data/primer_regions.bed" label="${tool.name} on ${on_string}: All candidate primer regions">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

249 <filter>mode['misc_outputs'] and 'primer_regions' in mode['misc_outputs']</filter>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

250 </data>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

251 <data name="probe_regions" format="bed" from_work_dir="results/data/probe_regions.bed" label="${tool.name} on ${on_string}: All candidate qPCR probe regions">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

252 <filter>mode['misc_outputs'] and 'probe_regions' in mode['misc_outputs']</filter>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

253 </data>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

254 <data name="all_primers" format="bed" from_work_dir="results/data/all_primers.bed" label="${tool.name} on ${on_string}: All primer sites">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

255 <filter>mode['misc_outputs'] and 'all_primers' in mode['misc_outputs']</filter>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

256 </data>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

257 </outputs>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

258 <tests>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

259 <test expect_num_outputs="8">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

260 <param name="alignment" value="hepatitis_e_aln_shrunk.fasta"/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

261 <conditional name="mode">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

262 <param name='m_select' value="single"/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

263 <conditional name="main_params">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

264 <param name="specify_how" value="set_both"/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

265 <param name="threshold" value="0.8"/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

266 <param name="n_ambig" value="3"/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

267 </conditional>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

268 <param name="opt_length" value="300"/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

269 <param name="max_length" value="400"/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

270 <conditional name="limit_report">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

271 <param name="choice" value="yes" />

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

272 <param name="report_n" value="5"/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

273 </conditional>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

274 </conditional>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

275 <output name="varvamp_log" ftype="txt" compare="contains" file="test1.log" />

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

276 <output name="ambiguous_consensus" ftype="fasta" file="ambiguous_consensus.fasta" />

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

277 <output name="amplicon_plot" ftype="pdf">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

278 <assert_contents>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

279 <has_text text="%PDF"/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

280 <has_text text="%%EOF"/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

281 </assert_contents>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

282 </output>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

283 <output name="primers_bed" ftype="bed">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

284 <assert_contents>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

285 <has_n_lines n="2" />

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

286 </assert_contents>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

287 </output>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

288 <output name="amplicons_bed" ftype="bed">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

289 <assert_contents>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

290 <has_n_lines n="1"/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

291 </assert_contents>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

292 </output>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

293 <output name="per_base_mismatches" ftype="pdf">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

294 <assert_contents>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

295 <has_text text="%PDF"/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

296 <has_text text="%%EOF"/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

297 </assert_contents>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

298 </output>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

299 <output name="primer_seqs" ftype="fasta">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

300 <assert_contents>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

301 <has_line line=">AMPLICON_0_LEFT"/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

302 <has_line line=">AMPLICON_0_RIGHT"/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

303 <has_n_lines n="4"/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

304 </assert_contents>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

305 </output>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

306 </test>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

307 <test expect_num_outputs="12">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

308 <param name="alignment" value="hepatitis_e_aln_shrunk.fasta"/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

309 <conditional name="mode">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

310 <param name='m_select' value="tiled"/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

311 <conditional name="main_params">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

312 <param name="specify_how" value="set_both"/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

313 <param name="threshold" value="0.6"/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

314 <param name="n_ambig" value="2"/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

315 </conditional>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

316 <param name="opt_length" value="150"/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

317 <param name="max_length" value="300"/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

318 <param name="overlap" value="100"/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

319 </conditional>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

320 <output name="varvamp_log" ftype="txt" compare="contains" file="test2.log" />

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

321 <output name="primers_bed" ftype="bed">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

322 <assert_contents>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

323 <has_n_lines n="4" />

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

324 </assert_contents>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

325 </output>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

326 <output name="amplicons_bed" ftype="bed">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

327 <assert_contents>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

328 <has_n_lines n="2"/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

329 </assert_contents>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

330 </output>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

331 <output name="primer_amplicon_assignments" ftype="tabular">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

332 <assert_contents>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

333 <has_n_lines n="2"/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

334 <has_n_columns n="2"/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

335 </assert_contents>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

336 </output>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

337 <output name="unresolved_primer_dimers" ftype="tabular">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

338 <assert_contents>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

339 <has_n_lines n="1"/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

340 </assert_contents>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

341 </output>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

342 <output_collection name="primer_seqs_collection" type="list" count="2">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

343 <element name="pool1_sequences" ftype="fasta">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

344 <assert_contents>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

345 <has_n_lines n="4"/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

346 <has_line line=">AMPLICON_0_LEFT"/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

347 </assert_contents>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

348 </element>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

349 <element name="pool2_sequences" ftype="fasta">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

350 <assert_contents>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

351 <has_n_lines n="4"/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

352 <has_line line=">AMPLICON_1_LEFT"/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

353 </assert_contents>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

354 </element>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

355 </output_collection>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

356 </test>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

357 <test expect_num_outputs="9">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

358 <param name="alignment" value="hepatitis_e_aln_shrunk.fasta"/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

359 <conditional name="mode">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

360 <param name='m_select' value="qpcr"/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

361 <conditional name="main_params">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

362 <param name="specify_how" value="set_both"/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

363 <param name="threshold" value="0.7"/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

364 <param name="n_ambig" value="1"/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

365 <param name="pn_ambig" value="1"/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

366 </conditional>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

367 <param name="test_n" value="180"/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

368 <param name="deltaG" value="-15"/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

369 </conditional>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

370 <output name="varvamp_log" ftype="txt" compare="contains" file="test3.log" />

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

371 <output name="primers_bed" ftype="bed">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

372 <assert_contents>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

373 <has_n_lines n="3" />

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

374 </assert_contents>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

375 </output>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

376 <output name="amplicons_bed" ftype="bed">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

377 <assert_contents>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

378 <has_n_lines n="1"/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

379 </assert_contents>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

380 </output>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

381 <output name="primer_seqs" ftype="fasta">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

382 <assert_contents>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

383 <has_line line=">QPCR_SCHEME_0_PROBE"/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

384 <has_line line=">QPCR_SCHEME_0_LEFT"/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

385 <has_line line=">QPCR_SCHEME_0_RIGHT"/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

386 <has_n_lines n="6"/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

387 </assert_contents>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

388 </output>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

389 <output name="qpcr_details" ftype="tabular">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

390 <assert_contents>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

391 <has_n_lines n="2"/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

392 </assert_contents>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

393 </output>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

394 </test>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

395 <test expect_num_outputs="1">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

396 <!-- Similar to test 1, but try to modify some of varVAMP's

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

397 advanced params, and see whether that gets reflected in the log file.

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

398 -->

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

399 <param name="alignment" value="hepatitis_e_aln_shrunk.fasta"/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

400 <conditional name="mode">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

401 <param name='m_select' value="single"/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

402 <conditional name="main_params">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

403 <param name="specify_how" value="set_both"/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

404 <param name="threshold" value="0.8"/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

405 <param name="n_ambig" value="3"/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

406 </conditional>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

407 <param name="opt_length" value="300"/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

408 <param name="max_length" value="400"/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

409 <conditional name="limit_report">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

410 <param name="choice" value="yes" />

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

411 <param name="report_n" value="5"/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

412 </conditional>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

413 <conditional name="advanced_config">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

414 <param name="customize" value="yes"/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

415 <section name="basic_primer_params">

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

416 <param name="PRIMER_GC_RANGE_min" value="20"/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

417 <param name="PRIMER_GC_RANGE_max" value="80"/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

418 </section>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

419 </conditional>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

420 <param name="scheme_outputs" value=""/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

421 <param name="aln_cons_outputs" value=""/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

422 <param name="plot_outputs" value=""/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

423 <param name="misc_outputs" value=""/>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

424 </conditional>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

425 <output name="varvamp_log" ftype="txt" compare="contains" file="test4.log" />

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

426 </test>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

427 </tests>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

428 <help><![CDATA[

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

429

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

430 .. class:: infomark

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

431

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

432 **What it does**

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

433

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

434 variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences.

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

435

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

436 For a lot of virus genera it is difficult to design pan-specific primers. varVAMP solves this by introducing ambiguous characters into primers and minimizes mismatches at the 3' end. Primers might not work for some sequences of your input alignment but should recognize the large majority.

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

437

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

438 varVAMP can be run in three different **modes**:

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

439

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

440 * SINGLE: varVAMP searches for the very best primers and reports back non-overlapping amplicons which can be used for PCR-based screening approaches.

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

441 * TILED: varVAMP uses a graph based approach to design overlapping (tiled) amplicons that together cover the entire viral genome. This designs amplicons that are suitable for Oxford Nanopore or Illumina based full-genome sequencing.

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

442 * QPCR: varVAMP searches for small amplicons with an optimized internal probe (TaqMan). It minimizes temperature differences between the primers and checks for amplicon secondary structures.

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

443

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

444 Algorithmic parameters:

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

445

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

446 These are explained very well on the `How varVAMP works <https://github.com/jonas-fuchs/varVAMP/blob/master/docs/how_varvamp_works.md>`__ page of the varVAMP documentation.

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

447

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

448 Outputs:

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

449

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

450 This tool can produce lots of informative output and the different modes come with what we hope are reasonable default choices.

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

451

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

452 The most important output, however, is the **Analysis Log**, which will always be generated and contains essential information about what parameters where used by varVAMP during the run and about intermediate results. You should always check this file. Together with the tool's standard output and error streams, it is the place to spot issues with your analysis and to start debugging them.

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

453

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

454 .. class:: infomark

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

455

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

456 Testing with a new alignment/analysis:

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

457

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

458 As a first check whether a new alignment of viral sequences can be used with specific settings of the tool, it may help to disable all configurable outputs, which will leave you with only the Analysis Log. This will be enough to see if there are any errors with the combination of alignment and settings, and whether you are on a roughly correct track (varVAMP reports some primers, for example). This way, you're not flooding your analysis history with lots of likely useless datasets, and once you've fixed potential issues you can add back more outputs and rerun the analysis.

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

459 ]]></help>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

460 <citations>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

461 <citation type="doi">https://github.com/jonas-fuchs/varVAMP/</citation>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

462 </citations>

462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

iuc

parents:

diff changeset

463 </tool>

Mercurial > repos > iuc > varvamp

annotate varvamp.xml @ 0:462e62be07e1 draft