varvamp: varvamp.xml annotate

annotate varvamp.xml @ 6:c1f08498cd74 draft default tip

planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 20fd2669164ff3cf1b77f732a801680473430805

author	iuc
date	Thu, 13 Feb 2025 09:20:17 +0000
parents	d6d746d0d1d0
children

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>
5 d6d746d0d1d0 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d iuc parents: 4 diff changeset	11 <requirement type="package" version="2.0.3">primer3-py</requirement>
1 80e18c0836e5 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 1626c59de1e3aa8a9ccb8674b38a4654a03ab44b iuc parents: 0 diff changeset	12 <requirement type="package" version="0.7.17">seqfold</requirement>
5 d6d746d0d1d0 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d iuc parents: 4 diff changeset	13 <requirement type="package" version="3.12">python</requirement>
d6d746d0d1d0 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d iuc parents: 4 diff changeset	14 <requirement type="package" version="9.5">coreutils</requirement>
0 462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	15 </requirements>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	16 <version_command>varvamp --version</version_command>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	17 <command detect_errors="exit_code"><![CDATA[
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	18 VARVAMP_CONFIG=custom_config varvamp
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	19
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	20 $mode.m_select
5 d6d746d0d1d0 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d iuc parents: 4 diff changeset	21 --name '$mode.name'
0 462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	22 #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	23 --threshold $mode.main_params.threshold
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 #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	26 --n-ambig $mode.main_params.n_ambig
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	27 #if $mode.m_select == "qpcr":
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	28 --pn-ambig $mode.main_params.pn_ambig
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	29 #end if
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	30 #end if
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	31 #if str( $mode.m_select ) == "single":
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	32 --opt-length $mode.opt_length
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	33 --max-length $mode.max_length
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	34 #if $mode.limit_report.choice == "yes":
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	35 --report-n $mode.limit_report.report_n
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	36 #end if
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	37 #elif str( $mode.m_select ) == "tiled":
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	38 --opt-length $mode.opt_length
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	39 --max-length $mode.max_length
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	40 --overlap $mode.overlap
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	41 #elif str( $mode.m_select ) == "qpcr":
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	42 --test-n $mode.test_n
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	43 --deltaG $mode.deltaG
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	44 #end if
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	45 #if $mode.filter_blast_hits.choice == "yes":
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	46 --database '${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	47 #end if
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	48 --threads \${GALAXY_SLOTS:-1}
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	49
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	50 '$alignment'
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	51 results/
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	52
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	53 #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	54 ## 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	55 && mv results/oligos.fasta results/primers.fasta
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	56 #end if
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	57 #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	58 ## 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
5 d6d746d0d1d0 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d iuc parents: 4 diff changeset	59 && cp --update=none dimers_fallback.tsv results/unsolvable_primer_dimers.tsv
0 462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	60 #end if
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	61 ]]></command>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	62 <configfiles>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	63 <configfile filename="custom_config"><![CDATA[#if $mode.advanced_config.customize == "yes":
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	64 PRIMER_TMP = ($mode.advanced_config.basic_primer_params.PRIMER_TMP_min, $mode.advanced_config.basic_primer_params.PRIMER_TMP_max, $mode.advanced_config.basic_primer_params.PRIMER_TMP_opt)
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	65 PRIMER_GC_RANGE = ($mode.advanced_config.basic_primer_params.PRIMER_GC_RANGE_min, $mode.advanced_config.basic_primer_params.PRIMER_GC_RANGE_max, $mode.advanced_config.basic_primer_params.PRIMER_GC_RANGE_opt)
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	66 PRIMER_SIZES = ($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	67 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	68 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	69 PRIMER_HAIRPIN = $mode.advanced_config.basic_primer_params.PRIMER_HAIRPIN
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	70 PRIMER_GC_END = ($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	71 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	72 PRIMER_MAX_DIMER_TMP = $mode.advanced_config.basic_primer_params.PRIMER_MAX_DIMER_TMP
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	73 #if str($mode.m_select) == "qpcr":
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	74 QPROBE_TMP = ($mode.advanced_config.qpcr_params.QPROBE_TMP_min, $mode.advanced_config.qpcr_params.QPROBE_TMP_max, $mode.advanced_config.qpcr_params.QPROBE_TMP_opt)
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	75 QPROBE_SIZES = ($mode.advanced_config.qpcr_params.QPROBE_SIZES_min, $mode.advanced_config.qpcr_params.QPROBE_SIZES_max, $mode.advanced_config.qpcr_params.QPROBE_SIZES_opt)
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	76 QPROBE_GC_RANGE = ($mode.advanced_config.qpcr_params.QPROBE_GC_RANGE_min, $mode.advanced_config.qpcr_params.QPROBE_GC_RANGE_max, $mode.advanced_config.qpcr_params.QPROBE_GC_RANGE_opt)
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	77 QPROBE_GC_END = ($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	78 QPRIMER_DIFF = $mode.advanced_config.qpcr_params.QPRIMER_DIFF
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	79 QPROBE_TEMP_DIFF = ($mode.advanced_config.qpcr_params.QPROBE_TEMP_DIFF_min, $mode.advanced_config.qpcr_params.QPROBE_TEMP_DIFF_max)
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	80 QPROBE_DISTANCE = ($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	81 END_OVERLAP = $mode.advanced_config.qpcr_params.END_OVERLAP
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	82 QAMPLICON_LENGTH = ($mode.advanced_config.qpcr_params.QAMPLICON_LENGTH_min, $mode.advanced_config.qpcr_params.QAMPLICON_LENGTH_max)
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	83 QAMPLICON_GC = ($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	84 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	85 #end if
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	86 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	87 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	88 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	89 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	90 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	91 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	92 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	93 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	94 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	95 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	96 #end if
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	97 #if $mode.filter_blast_hits.choice == "yes":
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	98 #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	99 BLAST_SETTINGS = {
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	100 "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	101 "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	102 "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	103 "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	104 "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	105 "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	106 }
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	107 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	108 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	109 #end if
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	110 #end if
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	111 ]]></configfile>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	112 <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	113 $line]]></configfile>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	114 </configfiles>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	115 <inputs>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	116 <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	117 <conditional name="mode">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	118 <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	119 <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	120 <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	121 <option value="qpcr">qPCR primers (qpcr)</option>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	122 </param>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	123 <when value="single">
5 d6d746d0d1d0 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d iuc parents: 4 diff changeset	124 <param argument="--name" type="text" value="AMPLICON" label="Name your amplicon" help="This name will be used in various outputs of the tool." />
0 462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	125 <expand macro="main_parameters" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	126 <expand macro="amplicon_length_restrictions" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	127 <expand macro="blast_options" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	128 <conditional name="limit_report">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	129 <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	130 <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	131 <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	132 </param>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	133 <when value="no" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	134 <when value="yes">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	135 <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	136 </when>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	137 </conditional>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	138 <expand macro="customize_advanced" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	139 <expand macro="primer_scheme_outputs">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	140 <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	141 </expand>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	142 <expand macro="consensus_outputs" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	143 <expand macro="graphical_outputs" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	144 <expand macro="miscellaneous_outputs">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	145 <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	146 </expand>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	147 </when>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	148 <when value="tiled">
5 d6d746d0d1d0 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d iuc parents: 4 diff changeset	149 <param argument="--name" type="text" value="TILED_SCHEME" label="Name your primer scheme" help="This name will be used in various outputs of the tool." />
0 462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	150 <expand macro="main_parameters" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	151 <expand macro="amplicon_length_restrictions" />
6 c1f08498cd74 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 20fd2669164ff3cf1b77f732a801680473430805 iuc parents: 5 diff changeset	152 <param argument="--overlap" type="integer" min="1" value="100" label="Minimal required overlap between tiled amplicon inserts" help="default: 100" />
0 462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	153 <expand macro="blast_options" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	154 <expand macro="customize_advanced" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	155 <expand macro="primer_scheme_outputs">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	156 <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	157 <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	158 </expand>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	159 <expand macro="consensus_outputs" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	160 <expand macro="graphical_outputs" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	161 <expand macro="miscellaneous_outputs">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	162 <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	163 </expand>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	164 </when>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	165 <when value="qpcr">
5 d6d746d0d1d0 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d iuc parents: 4 diff changeset	166 <param argument="--name" type="text" value="QPCR_SCHEME" label="Name your qPCR scheme" help="This name will be used in various outputs of the tool." />
0 462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	167 <expand macro="main_parameters">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	168 <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	169 </expand>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	170 <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	171 <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	172 <expand macro="blast_options" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	173 <expand macro="customize_advanced">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	174 <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	175 <!--basic probe parameters-->
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	176 <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	177 <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	178 <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	179 <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	180 <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	181 <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	182 <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	183 <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	184 <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	185 <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	186 <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	187 <!--constraints for amplicon design-->
4 36c91ff33d70 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 11f2603dc33eecd4fb6f6239143d13c53492fd86 iuc parents: 3 diff changeset	188 <param name="QPRIMER_DIFF" type="integer" min="0" value="2" label="Maximal melting temperature difference among qPCR primers" />
36c91ff33d70 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 11f2603dc33eecd4fb6f6239143d13c53492fd86 iuc parents: 3 diff changeset	189 <param name="QPROBE_TEMP_DIFF_min" type="integer" min="0" value="5" label="Minimal melting temperature difference between qPCR probe and primers" />
36c91ff33d70 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 11f2603dc33eecd4fb6f6239143d13c53492fd86 iuc parents: 3 diff changeset	190 <param name="QPROBE_TEMP_DIFF_max" type="integer" min="0" value="10" label="Maximal melting temperature difference between qPCR probe and primers" />
36c91ff33d70 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 11f2603dc33eecd4fb6f6239143d13c53492fd86 iuc parents: 3 diff changeset	191 <param name="QPROBE_DISTANCE_min" type="integer" min="0" value="4" label="Minimal distance of the qPCR probe from the primer on the same strand" />
36c91ff33d70 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 11f2603dc33eecd4fb6f6239143d13c53492fd86 iuc parents: 3 diff changeset	192 <param name="QPROBE_DISTANCE_max" type="integer" min="0" value="15" label="Maximal distance of the qPCR probe from the primer on the same strand" />
36c91ff33d70 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 11f2603dc33eecd4fb6f6239143d13c53492fd86 iuc parents: 3 diff changeset	193 <param name="END_OVERLAP" type="integer" min="0" value="5" label="End Overlap" help="Maximal overlap in bases between the ends of the qPCR probe and the primer on the opposite strand" />
36c91ff33d70 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 11f2603dc33eecd4fb6f6239143d13c53492fd86 iuc parents: 3 diff changeset	194 <param name="QAMPLICON_LENGTH_min" type="integer" min="0" value="70" label="Minimal length of qPCR amplicons" />
36c91ff33d70 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 11f2603dc33eecd4fb6f6239143d13c53492fd86 iuc parents: 3 diff changeset	195 <param name="QAMPLICON_LENGTH_max" type="integer" min="0" value="200" label="Maximal length of qPCR amplicons" />
0 462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	196 <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	197 <param name="QAMPLICON_GC_max" type="integer" min="0" max="100" value="60" label="Maximal GC-content of qPCR amplicons" />
4 36c91ff33d70 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 11f2603dc33eecd4fb6f6239143d13c53492fd86 iuc parents: 3 diff changeset	198 <param name="QAMPLICON_DEL_CUTOFF" type="integer" min="0" 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."/>
0 462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	199 </section>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	200 </expand>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	201 <expand macro="primer_scheme_outputs">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	202 <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	203 </expand>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	204 <expand macro="consensus_outputs" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	205 <expand macro="graphical_outputs" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	206 <expand macro="miscellaneous_outputs">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	207 <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	208 </expand>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	209 </when>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	210 </conditional>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	211 </inputs>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	212 <outputs>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	213 <data name="varvamp_log" format="txt" from_work_dir="results/varvamp_log.txt" label="${tool.name} on ${on_string}: Analysis Log" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	214 <data name="primer_seqs" format="fasta" from_work_dir="results/primers.fasta" label="${tool.name} on ${on_string}: Sequences of designed oligos">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	215 <filter>mode['m_select'] in ('single', 'qpcr') and mode['scheme_outputs'] and 'primer_seqs' in mode['scheme_outputs']</filter>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	216 </data>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	217 <collection name="primer_seqs_collection" type="list" label="${tool.name} on ${on_string}: per-pool primer sequences">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	218 <filter>mode['m_select'] == 'tiled' and mode['scheme_outputs'] and 'primer_seqs' in mode['scheme_outputs']</filter>
5 d6d746d0d1d0 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d iuc parents: 4 diff changeset	219 <data name="pool1_sequences" format="fasta" from_work_dir="results/primers_pool_1.fasta" label="${tool.name} on ${on_string}: Sequences of designed pool 1 primers" />
d6d746d0d1d0 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d iuc parents: 4 diff changeset	220 <data name="pool2_sequences" format="fasta" from_work_dir="results/primers_pool_2.fasta" label="${tool.name} on ${on_string}: Sequences of designed pool 2 primers" />
0 462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	221 </collection>
6 c1f08498cd74 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 20fd2669164ff3cf1b77f732a801680473430805 iuc parents: 5 diff changeset	222 <data name="primers_bed" format="bed" from_work_dir="results/primers.bed" label="${tool.name} on ${on_string}: Primer binding sites">
0 462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	223 <filter>mode['scheme_outputs'] and 'primer_binding_sites' in mode['scheme_outputs']</filter>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	224 </data>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	225 <data name="amplicons_bed" format="bed" from_work_dir="results/amplicons.bed" label="${tool.name} on ${on_string}: Amplicon locations">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	226 <filter>mode['scheme_outputs'] and 'amplicon_sites' in mode['scheme_outputs']</filter>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	227 </data>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	228 <data name="primers_details" format="tabular" from_work_dir="results/*primers.tsv" label="${tool.name} on ${on_string}: Primer details">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	229 <filter>mode['scheme_outputs'] and 'primer_details' in mode['scheme_outputs']</filter>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	230 </data>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	231 <data name="qpcr_details" format="tabular" from_work_dir="results/qpcr_design.tsv" label="${tool.name} on ${on_string}: qPCR amplicon details" >
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	232 <filter>mode['scheme_outputs'] and 'qpcr_design' in mode['scheme_outputs']</filter>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	233 </data>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	234 <data name="primer_amplicon_assignments" format="tabular" from_work_dir="results/primer_to_amplicon_assignment.tabular" label="${tool.name} on ${on_string}: Primer to amplicon assignments">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	235 <filter>mode['scheme_outputs'] and 'amplicon_assignment' in mode['scheme_outputs']</filter>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	236 </data>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	237 <data name="unresolved_primer_dimers" format="tabular" from_work_dir="results/unsolvable_primer_dimers.tsv" label="${tool.name} on ${on_string}: Unresolved primer dimers">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	238 <filter>mode['scheme_outputs'] and 'primer_dimers' in mode['scheme_outputs']</filter>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	239 </data>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	240 <data name="ambiguous_consensus" format="fasta" from_work_dir="results/ambiguous_consensus.fasta" label="${tool.name} on ${on_string}: Ambiguous consensus sequence">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	241 <filter>mode['aln_cons_outputs'] and 'ambiguous_consensus' in mode['aln_cons_outputs']</filter>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	242 </data>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	243 <data name="majority_consensus" format="fasta" from_work_dir="results/data/majority_consensus.fasta" label="${tool.name} on ${on_string}: Majority consensus sequence (no ambiguity codes)">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	244 <filter>mode['aln_cons_outputs'] and 'majority_consensus' in mode['aln_cons_outputs']</filter>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	245 </data>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	246 <data name="alignment_cleaned" format="fasta" from_work_dir="results/data/alignment_cleaned.fasta" label="${tool.name} on ${on_string}: Alignment cleaned">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	247 <filter>mode['aln_cons_outputs'] and 'alignment_cleaned' in mode['aln_cons_outputs']</filter>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	248 </data>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	249 <data name="amplicon_plot" format="pdf" from_work_dir="results/amplicon_plot.pdf" label="${tool.name} on ${on_string}: Amplicon design overview plot">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	250 <filter>mode['plot_outputs'] and 'amplicon_plot' in mode['plot_outputs']</filter>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	251 </data>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	252 <data name="per_base_mismatches" format="pdf" from_work_dir="results/per_base_mismatches.pdf" label="${tool.name} on ${on_string}: Per-base mismatches barplots">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	253 <filter>mode['plot_outputs'] and 'per_base_mismatches' in mode['plot_outputs']</filter>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	254 </data>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	255 <data name="primer_regions" format="bed" from_work_dir="results/data/primer_regions.bed" label="${tool.name} on ${on_string}: All candidate primer regions">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	256 <filter>mode['misc_outputs'] and 'primer_regions' in mode['misc_outputs']</filter>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	257 </data>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	258 <data name="probe_regions" format="bed" from_work_dir="results/data/probe_regions.bed" label="${tool.name} on ${on_string}: All candidate qPCR probe regions">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	259 <filter>mode['misc_outputs'] and 'probe_regions' in mode['misc_outputs']</filter>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	260 </data>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	261 <data name="all_primers" format="bed" from_work_dir="results/data/all_primers.bed" label="${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	262 <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	263 </data>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	264 </outputs>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	265 <tests>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	266 <test expect_num_outputs="8">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	267 <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	268 <conditional name="mode">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	269 <param name='m_select' value="single"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	270 <conditional name="main_params">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	271 <param name="specify_how" value="set_both"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	272 <param name="threshold" value="0.8"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	273 <param name="n_ambig" value="3"/>
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 <param name="opt_length" value="300"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	276 <param name="max_length" value="400"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	277 <conditional name="limit_report">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	278 <param name="choice" value="yes" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	279 <param name="report_n" value="5"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	280 </conditional>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	281 </conditional>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	282 <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	283 <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	284 <output name="amplicon_plot" ftype="pdf">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	285 <assert_contents>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	286 <has_text text="%PDF"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	287 <has_text text="%%EOF"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	288 </assert_contents>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	289 </output>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	290 <output name="primers_bed" ftype="bed">
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 <has_n_lines n="2" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	293 </assert_contents>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	294 </output>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	295 <output name="amplicons_bed" ftype="bed">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	296 <assert_contents>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	297 <has_n_lines n="1"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	298 </assert_contents>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	299 </output>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	300 <output name="per_base_mismatches" ftype="pdf">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	301 <assert_contents>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	302 <has_text text="%PDF"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	303 <has_text text="%%EOF"/>
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 <output name="primer_seqs" ftype="fasta">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	307 <assert_contents>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	308 <has_line line=">AMPLICON_0_LEFT"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	309 <has_line line=">AMPLICON_0_RIGHT"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	310 <has_n_lines n="4"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	311 </assert_contents>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	312 </output>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	313 </test>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	314 <test expect_num_outputs="12">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	315 <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	316 <conditional name="mode">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	317 <param name='m_select' value="tiled"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	318 <conditional name="main_params">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	319 <param name="specify_how" value="set_both"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	320 <param name="threshold" value="0.6"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	321 <param name="n_ambig" value="2"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	322 </conditional>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	323 <param name="opt_length" value="150"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	324 <param name="max_length" value="300"/>
6 c1f08498cd74 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 20fd2669164ff3cf1b77f732a801680473430805 iuc parents: 5 diff changeset	325 <param name="overlap" value="76"/>
0 462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	326 </conditional>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	327 <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	328 <output name="primers_bed" ftype="bed">
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 <has_n_lines n="4" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	331 </assert_contents>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	332 </output>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	333 <output name="amplicons_bed" ftype="bed">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	334 <assert_contents>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	335 <has_n_lines n="2"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	336 </assert_contents>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	337 </output>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	338 <output name="primer_amplicon_assignments" ftype="tabular">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	339 <assert_contents>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	340 <has_n_lines n="2"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	341 <has_n_columns n="2"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	342 </assert_contents>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	343 </output>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	344 <output name="unresolved_primer_dimers" ftype="tabular">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	345 <assert_contents>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	346 <has_n_lines n="1"/>
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 </output>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	349 <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	350 <element name="pool1_sequences" ftype="fasta">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	351 <assert_contents>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	352 <has_n_lines n="4"/>
5 d6d746d0d1d0 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d iuc parents: 4 diff changeset	353 <has_line line=">TILED_SCHEME_0_LEFT"/>
0 462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	354 </assert_contents>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	355 </element>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	356 <element name="pool2_sequences" ftype="fasta">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	357 <assert_contents>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	358 <has_n_lines n="4"/>
5 d6d746d0d1d0 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 938f80815419af5d560f949d884989cf1d69550d iuc parents: 4 diff changeset	359 <has_line line=">TILED_SCHEME_1_LEFT"/>
0 462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	360 </assert_contents>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	361 </element>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	362 </output_collection>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	363 </test>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	364 <test expect_num_outputs="9">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	365 <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	366 <conditional name="mode">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	367 <param name='m_select' value="qpcr"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	368 <conditional name="main_params">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	369 <param name="specify_how" value="set_both"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	370 <param name="threshold" value="0.7"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	371 <param name="n_ambig" value="1"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	372 <param name="pn_ambig" value="1"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	373 </conditional>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	374 <param name="test_n" value="180"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	375 <param name="deltaG" value="-15"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	376 </conditional>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	377 <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	378 <output name="primers_bed" ftype="bed">
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 <has_n_lines n="3" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	381 </assert_contents>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	382 </output>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	383 <output name="amplicons_bed" ftype="bed">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	384 <assert_contents>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	385 <has_n_lines n="1"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	386 </assert_contents>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	387 </output>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	388 <output name="primer_seqs" ftype="fasta">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	389 <assert_contents>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	390 <has_line line=">QPCR_SCHEME_0_PROBE"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	391 <has_line line=">QPCR_SCHEME_0_LEFT"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	392 <has_line line=">QPCR_SCHEME_0_RIGHT"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	393 <has_n_lines n="6"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	394 </assert_contents>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	395 </output>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	396 <output name="qpcr_details" ftype="tabular">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	397 <assert_contents>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	398 <has_n_lines n="2"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	399 </assert_contents>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	400 </output>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	401 </test>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	402 <test expect_num_outputs="1">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	403 <!-- 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	404 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	405 -->
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	406 <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	407 <conditional name="mode">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	408 <param name='m_select' value="single"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	409 <conditional name="main_params">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	410 <param name="specify_how" value="set_both"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	411 <param name="threshold" value="0.8"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	412 <param name="n_ambig" value="3"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	413 </conditional>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	414 <param name="opt_length" value="300"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	415 <param name="max_length" value="400"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	416 <conditional name="limit_report">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	417 <param name="choice" value="yes" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	418 <param name="report_n" value="5"/>
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 <conditional name="advanced_config">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	421 <param name="customize" value="yes"/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	422 <section name="basic_primer_params">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	423 <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	424 <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	425 </section>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	426 </conditional>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	427 <param name="scheme_outputs" value=""/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	428 <param name="aln_cons_outputs" value=""/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	429 <param name="plot_outputs" value=""/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	430 <param name="misc_outputs" value=""/>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	431 </conditional>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	432 <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	433 </test>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	434 </tests>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	435 <help><![CDATA[
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	436
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	437 .. class:: infomark
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	438
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	439 What it does
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	440
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	441 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	442
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	443 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	444
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	445 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	446
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	447 * 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	448 * 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	449 * 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	450
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	451 Algorithmic parameters:
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	452
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	453 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	454
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	455 Outputs:
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	456
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	457 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	458
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	459 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	460
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	461 .. class:: infomark
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	462
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	463 Testing with a new alignment/analysis:
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	464
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	465 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	466 ]]></help>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	467 <citations>
1 80e18c0836e5 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 1626c59de1e3aa8a9ccb8674b38a4654a03ab44b iuc parents: 0 diff changeset	468 <citation type="doi">10.5281/zenodo.10908223</citation>
0 462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	469 </citations>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d iuc parents: diff changeset	470 </tool>

Mercurial > repos > iuc > varvamp

annotate varvamp.xml @ 6:c1f08498cd74 draft default tip