Mercurial > repos > iuc > pureclip

annotate pureclip.xml @ 2:75bf02d7d1c8 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit c4a054d38cb9fe724612ba666f5a6d3e3ef49e75
author iuc
date Thu, 21 Jul 2022 19:17:57 +0000
parents fd1f57782683
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
75bf02d7d1c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit c4a054d38cb9fe724612ba666f5a6d3e3ef49e75
iuc
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diff changeset
1 <tool id="pureclip" name="PureCLIP" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.01">
0
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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2 <description>- HMM based peak caller designed for eCLIP/iCLIP data</description>
2
75bf02d7d1c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit c4a054d38cb9fe724612ba666f5a6d3e3ef49e75
iuc
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3 <macros>
75bf02d7d1c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit c4a054d38cb9fe724612ba666f5a6d3e3ef49e75
iuc
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4 <token name="@TOOL_VERSION@">1.0.4</token>
75bf02d7d1c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit c4a054d38cb9fe724612ba666f5a6d3e3ef49e75
iuc
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5 <token name="@VERSION_SUFFIX@">1</token>
75bf02d7d1c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit c4a054d38cb9fe724612ba666f5a6d3e3ef49e75
iuc
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6 </macros>
0
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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7 <requirements>
2
75bf02d7d1c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit c4a054d38cb9fe724612ba666f5a6d3e3ef49e75
iuc
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8 <requirement type="package" version="@TOOL_VERSION@">pureclip</requirement>
0
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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9 </requirements>
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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10 <command detect_errors="exit_code"><![CDATA[
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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11 ln -s '${target_bam_file}' target.bam &&
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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12 ln -f -s '${target_bam_file.metadata.bam_index}' target.bam.bai &&
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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13 ln -s '${genome_fasta_file}' genome.fa &&
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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14 #if $control_bam_file:
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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15 ln -s '${control_bam_file}' control.bam &&
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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16 ln -f -s '${control_bam_file.metadata.bam_index}' control.bam.bai &&
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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17 #end if
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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18 #if $motif_data.motif_data_selector == 'supply_CL_motifs':
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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19 ln -s '${motif_data.cl_motif_bed_file}' motif_hits.bed &&
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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20 #end if
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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21
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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22 pureclip
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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23 -o crosslink_sites.bed
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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24 -or binding_regions.bed
1
fd1f57782683 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit 169070069ea93f8cb57d660974c86baff0178b13
iuc
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25 -nt \${GALAXY_SLOTS:-1}
0
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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26 -i target.bam
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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27 -bai target.bam.bai
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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28 -g genome.fa
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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29 #if $learn_params_contigs
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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30 -iv '$learn_params_contigs'
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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31 #end if
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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32 #if $apply_hmm_contigs
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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33 -iv '$apply_hmm_contigs'
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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34 #end if
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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35 -dm $merge_dist
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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36 #if $control_bam_file:
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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37 -ibam control.bam
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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38 -ibai control.bam.bai
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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39 #end if
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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40 #if $motif_data.motif_data_selector == 'supply_CL_motifs':
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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41 -fis motif_hits.bed
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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42 -nim $motif_data.max_motif_id
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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43 #end if
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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44 #if $bc_data.bc_data_selector == 'bc_0':
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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45 -bc 0
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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46 #elif $bc_data.bc_data_selector == 'bc_1':
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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47 -bc 1
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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48 #elif $bc_data.bc_data_selector == 'manual_setting':
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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49 -bw $bc_data.bandwidth
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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50 -bwn $bc_data.bandwidthn
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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51 -b1p $bc_data.b1p
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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52 -b2p $bc_data.b2p
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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53 #if $bc_data.antp_option.antp_option_selector == 'antp_select':
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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54 -antp
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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55 #elif $bc_data.antp_option.antp_option_selector == 'manual_select':
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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56 -ntp $bc_data.antp_option.ntp
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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57 -ntp2 $bc_data.antp_option.ntp2
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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58 #end if
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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59 #end if
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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60 #if $advanced_params.advanced_params_selector == 'ap_specify':
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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61 $advanced_params.ld_precision
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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62 $advanced_params.use_viterbi
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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63 #if $advanced_params.max_iter_brent
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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64 -m $advanced_params.max_iter_brent
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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65 #end if
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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66 #if $advanced_params.max_iter_bw
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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67 -w $advanced_params.max_iter_bw
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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68 #end if
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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69 #if $advanced_params.g1kmin
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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70 -g1kmin $advanced_params.g1kmin
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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71 #end if
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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72 #if $advanced_params.g1kmax
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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73 -g1kmax $advanced_params.g1kmax
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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74 #end if
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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75 #if $advanced_params.g2kmin
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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76 -g2kmin $advanced_params.g2kmin
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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77 #end if
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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78 #if $advanced_params.g2kmax
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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79 -g2kmax $advanced_params.g2kmax
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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80 #end if
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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81 $advanced_params.fk
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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82 -mkn $advanced_params.mkn
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
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83 -mtp $advanced_params.mtp
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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84 #if $advanced_params.mk
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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85 -mk $advanced_params.mk
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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86 #end if
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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87 #if $advanced_params.pa
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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88 -pa $advanced_params.pa
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diff changeset
89 #end if
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diff changeset
90 $advanced_params.ea1
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diff changeset
91 $advanced_params.ea2
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diff changeset
92 $advanced_params.et1
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diff changeset
93 $advanced_params.et2
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diff changeset
94 #if $advanced_params.mrtf
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95 -mrtf $advanced_params.mrtf
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96 #end if
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diff changeset
97 -mtc $advanced_params.mtc
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diff changeset
98 -pet $advanced_params.pet
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99 #end if
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diff changeset
100 ]]></command>
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diff changeset
101 <inputs>
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102 <param name="target_bam_file" type="data" format="bam" label="Target BAM file" argument="-i"/>
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103 <param name="genome_fasta_file" type="data" format="fasta" label="Genome reference file" argument="-g"/>
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104 <!-- Options -->
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105 <param name="learn_params_contigs" type="text" optional="True"
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106 label="Genomic chromosomes to learn HMM parameters" argument="-iv"
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107 help="Genomic chromosomes to learn HMM parameters, e.g. 'chr1;chr2;chr3'. Contigs have to be in the same order as in BAM file. Useful to reduce runtime and memory consumption. Default: all contigs from reference file are used (useful when applying to transcript-wise alignments or poor data).">
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108 <sanitizer>
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109 <valid initial="string.printable">
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110 <remove value="&apos;"/>
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111 </valid>
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112 </sanitizer>
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113 </param>
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114 <param name="apply_hmm_contigs" type="text" label="Contigs to apply HMM" argument="-chr" optional="True"
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115 help="Contigs to apply HMM, e.g. 'chr1;chr2;chr3;'. Contigs have to be in the same order as in BAM file.">
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116 <sanitizer>
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117 <valid initial="string.printable">
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diff changeset
118 <remove value="&apos;"/>
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diff changeset
119 </valid>
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diff changeset
120 </sanitizer>
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121 </param>
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122 <param name="merge_dist" type="integer" value="8" min="1"
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123 label="Distance used to merge individual crosslink sites to binding regions" argument="-dm"/>
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124 <param name="control_bam_file" type="data" format="bam" optional="True"
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125 label="BAM file containing mapped reads from control experiment" argument="-ibam"
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126 help="Mapped reads in BAM format from a control experiment, e.g. eCLIP input"/>
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127 <conditional name="motif_data">
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128 <param name="motif_data_selector" type="select" label="Crosslink-associated (CL) motif options">
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129 <option value="no_CL_motifs_available" selected="true">No CL motifs available</option>
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130 <option value="supply_CL_motifs">Supply CL motifs</option>
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diff changeset
131 </param>
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132 <when value="no_CL_motifs_available" />
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133 <when value="supply_CL_motifs">
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134 <param name="cl_motif_bed_file" type="data" format="bed"
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135 label="FIMO input motif score covariates file" argument="-fis"
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diff changeset
136 help="FIMO input motif score covariates file"/>
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137 <param name="max_motif_id" type="integer" value="1"
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138 label="Max. motif ID to use" argument="-nim"
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diff changeset
139 help="Max. motif ID to use (Default: only covariates with motif ID 1 are used)"/>
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140 </when>
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141 </conditional>
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142
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143 <conditional name="bc_data">
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144 <param name="bc_data_selector" type="select" label="Define protein binding characteristics">
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145 <option value="bc_0" selected="true">RBP with short defined binding regions (-bc 0)</option>
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146 <option value="bc_1">RBP with larger crosslink clusters and lower read start counts (-bc 1)</option>
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147 <option value="manual_setting">Manual setting</option>
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148 </param>
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diff changeset
149 <when value="bc_0" />
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diff changeset
150 <when value="bc_1" />
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diff changeset
151 <when value="manual_setting">
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152 <param name="bandwidth" type="integer" value="50" min="1" max="500"
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153 label="Bandwidth for kernel density estimation used to access enrichment" argument="-bw"
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154 help="NOTE: Increasing the bandwidth increases runtime and memory consumption"/>
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155 <param name="bandwidthn" type="integer" value="50" min="1" max="500"
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156 label="Bandwidth for kernel density estimation used to estimate n for binomial distributions" argument="-bwn"
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diff changeset
157 help="For proteins that rather slide along the RNA or show long crosslink clusters increase -bwn, e.g. to 100 (should be LE 4*bw)"/>
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158 <param argument="-b1p" type="float" value="0.01"
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159 label="Initial value for binomial probability parameter of 'non-crosslink' state" />
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160 <param argument="-b2p" type="float" value="0.15"
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161 label="Initial value for binomial probability parameter of 'crosslink' state" />
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162 <conditional name="antp_option">
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163 <param name="antp_option_selector" type="select" label="Choose n threshold for estimating crosslink state parameters" help="Either automatically choose n threshold (-ntp, -ntp2) to estimate parameters linked to crosslink states based on expected read start count at crosslink sites, or manually set values">
eb000bccef28 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
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164 <option value="antp_select" selected="true">Automatically choose n threshold (-ntp, -ntp2)</option>
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165 <option value="manual_select">Manually set -ntp, -ntp2</option>
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166 </param>
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diff changeset
167 <when value="antp_select" />
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diff changeset
168 <when value="manual_select">
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169 <param argument="-ntp" type="integer" value="10"
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170 label="Only sites with n >= ntp are used to learn binomial probability parameters"/>
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171 <param argument="-ntp2" type="integer" value="0"
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172 label="Only sites with n >= ntp2 are used to learn probability of transition from state '2' to '2' or '3'"
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173 help="Useful for data with low truncation rates at crosslink sites or in general high fraction of non-coinciding read starts"/>
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174 </when>
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175 </conditional>
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176 </when>
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177 </conditional>
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178 <conditional name="advanced_params">
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179 <param name="advanced_params_selector" type="select" label="Additional advanced parameters">
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180 <option value="ap_not_specify" selected="true">Do not specify</option>
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181 <option value="ap_specify">Manually specify</option>
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182 </param>
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183 <when value="ap_not_specify" />
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184 <when value="ap_specify">
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185 <param name="ld_precision" label="Use higher precision to compute emission probabilities (long double)" type="boolean"
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186 truevalue="-ld" falsevalue="" checked="False"
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187 help="Useful in cases of extreme outliers, e.g. extreme high read start counts whose emission probabilities are close to zero and which would be discarded in default setting (along with warning messages). Note: increases memory consumption. Use in combination with '-iv' (default: double)"/>
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188 <param name="use_viterbi" label="Use Viterbi instead of posterior decoding"
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189 type="boolean" truevalue="-vtb" falsevalue="" checked="False"/>
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190 <param name="max_iter_brent" type="integer" optional="True" min="1" max="1000"
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191 label="Maximum number of iterations within BRENT algorithm" argument="-m"/>
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192 <param name="max_iter_bw" type="integer" optional="True" min="0" max="500"
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193 label="Maximum number of iterations within Baum-Welch algorithm" argument="-w"/>
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194 <param argument="-g1kmin" type="float" optional="True"
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195 label="Minimum shape k of 'non-enriched' gamma distribution" />
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196 <param argument="-g1kmax" type="float" optional="True"
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197 label="Maximum shape k of 'non-enriched' gamma distribution" />
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198 <param argument="-g2kmin" type="float" optional="True"
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199 label="Minimum shape k of 'enriched' gamma distribution" />
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200 <param argument="-g2kmax" type="float" optional="True"
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201 label="Maximum shape k of 'enriched' gamma distribution" />
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202 <param argument="-fk" label="Do not constrain 'non-enriched' shape parameter k"
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203 type="boolean" truevalue="-fk" falsevalue="" checked="False"
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204 help="When incorporating input signal, do not constrain 'non-enriched' shape parameter k LE 'enriched' gamma parameter k"/>
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205 <param argument="-mkn" type="float" value="1.0" min="0.5" max="1.5"
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206 label="Max. k/N ratio (read start sites/N) used to learn truncation probabilities for 'non-crosslink' and 'crosslink' emission probabilities"
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207 help="NOTE: high ratios might originate from mapping artifacts that can disturb parameter learning"/>
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208 <param argument="-mtp" type="float" value="0.0001"
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209 label="Min. transition probability from state '2' to '3'"
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210 help="Helpful for poor data, where no clear distinction between 'enriched' and 'non-enriched' is possible"/>
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211 <param argument="-mk" type="float" optional="True"
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212 label="Minimum KDE value used for fitting left-truncated gamma distributions"
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213 help="Default: corresponding to singleton read start."/>
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214 <param argument="-pa" type="integer" optional="True"
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215 label="Length threshold for internal poly-X stretches to get excluded" />
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216 <param argument="-ea1" label="Exclude intervals containing poly-A stretches from learning"
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217 type="boolean" truevalue="-ea1" falsevalue="" checked="False"/>
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218 <param argument="-ea2" label="Exclude intervals containing poly-A stretches from analysis"
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219 type="boolean" truevalue="-ea2" falsevalue="" checked="False"/>
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220 <param argument="-et1" label="Exclude intervals containing poly-U stretches from learning"
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221 type="boolean" truevalue="-et1" falsevalue="" checked="False"/>
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222 <param argument="-et2" label="Exclude intervals containing poly-U stretches from analysis"
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223 type="boolean" truevalue="-et2" falsevalue="" checked="False"/>
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224 <param argument="-mrtf" type="float" optional="True"
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225 label="Fit gamma shape k only for positions with min. covariate value" />
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226 <param argument="-mtc" type="integer" value="250" min="50" max="500"
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227 label="Maximum number of truncations at one position used for learning"
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228 help="NOTE: for sites with counts above threshold the whole covered regions will be ignored for learning!"/>
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229 <param argument="-pet" type="integer" value="7" min="2" max="50"
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230 label="Prior enrichment threshold"
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231 help="A KDE threshold corresponding to -pet read start counts at one position will be used for initial classification of 'non-enriched' and 'enriched' site"/>
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232 </when>
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233 </conditional>
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234 <section name="output_options" title="Additional output options">
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235 <param name="crosslink_bed_stats" type="boolean" value="False" label="Output learned parameter statistics file?"/>
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236 </section>
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237 </inputs>
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238 <outputs>
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239 <data format="bed" name="crosslink_bed_outfile" label="${tool.name} on ${on_string} crosslink sites (bed)" from_work_dir="crosslink_sites.bed"/>
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240 <data format="bed" name="binding_region_bed_outfile" label="${tool.name} on ${on_string} binding regions (bed)" from_work_dir="binding_regions.bed"/>
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241 <data format="txt" name="crosslink_bed_stats" label="${tool.name} on ${on_string} learned parameter statistcs (txt)" from_work_dir="crosslink_sites.bed.stats">
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242 <filter>(output_options['crosslink_bed_stats'] is True)</filter>
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243 </data>
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244 </outputs>
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245 <tests>
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246 <test>
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247 <param name="target_bam_file" value="aligned.prepro.R2.chrM:4000-8300.bam" ftype="bam"/>
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248 <param name="genome_fasta_file" value="hsa_chrM.fa" ftype="fasta"/>
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249 <param name="crosslink_bed_stats" value="True"/>
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250 <output name="crosslink_bed_outfile" file="chrM:4000-8300.crosslink_sites.bed"/>
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251 <output name="binding_region_bed_outfile" file="chrM:4000-8300.binding_regions.bed"/>
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252 <output name="crosslink_bed_stats" file="chrM:4000-8300.crosslink_sites.bed.stats"/>
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253 </test>
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254 <test>
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255 <param name="target_bam_file" value="aligned.prepro.R2.chrM:4000-8300.bam" ftype="bam"/>
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256 <param name="genome_fasta_file" value="hsa_chrM.fa" ftype="fasta"/>
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257 <param name="control_bam_file" value="input.aligned.prepro.R2.chrM:4000-8300.bam" ftype="bam"/>
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258 <param name="crosslink_bed_stats" value="True"/>
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259 <output name="crosslink_bed_outfile" file="chrM:4000-8300.crosslink_sites.cov_input_signal.bed"/>
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260 <output name="binding_region_bed_outfile" file="chrM:4000-8300.binding_regions.cov_input_signal.bed"/>
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261 <output name="crosslink_bed_stats" file="chrM:4000-8300.crosslink_sites.cov_input_signal.bed.stats"/>
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262 </test>
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263 <test>
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264 <param name="target_bam_file" value="aligned.prepro.R2.chrM:4000-8300.bam" ftype="bam"/>
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265 <param name="genome_fasta_file" value="hsa_chrM.fa" ftype="fasta"/>
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266 <param name="motif_data_selector" value="supply_CL_motifs"/>
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267 <param name="cl_motif_bed_file" value="fimo_clmotif_occurences.chrM:4000-8300.bed" ftype="bed"/>
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268 <param name="max_motif_id" value="4"/>
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269 <param name="crosslink_bed_stats" value="True"/>
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270 <output name="crosslink_bed_outfile" file="chrM:4000-8300.crosslink_sites.cov_CLmotifs.bed" compare="re_match"/>
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271 <output name="binding_region_bed_outfile" file="chrM:4000-8300.binding_regions.cov_CLmotifs.bed" compare="re_match"/>
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272 <output name="crosslink_bed_stats" file="chrM:4000-8300.crosslink_sites.cov_CLmotifs.bed.stats" compare="re_match"/>
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273 </test>
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274 <test>
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275 <param name="target_bam_file" value="aligned.prepro.R2.chrM:4000-8300.bam" ftype="bam"/>
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276 <param name="genome_fasta_file" value="hsa_chrM.fa" ftype="fasta"/>
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277 <param name="control_bam_file" value="input.aligned.prepro.R2.chrM:4000-8300.bam" ftype="bam"/>
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278 <param name="bc_data_selector" value="manual_setting"/>
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279 <param name="bandwidthn" value="50"/>
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280 <param name="b1p" value="0.01"/>
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281 <param name="b2p" value="0.15"/>
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282 <param name="antp_option_selector" value="manual_select"/>
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283 <param name="ntp" value="10"/>
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284 <param name="ntp2" value="0"/>
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285 <param name="advanced_params_selector" value="ap_specify"/>
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286 <param name="fk" value="True"/>
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287 <param name="mkn" value="0.9"/>
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288 <param name="mtc" value="200"/>
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289 <param name="crosslink_bed_stats" value="True"/>
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290 <output name="crosslink_bed_outfile" file="chrM:4000-8300.crosslink_sites.test4.bed"/>
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291 <output name="binding_region_bed_outfile" file="chrM:4000-8300.binding_regions.test4.bed"/>
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292 <output name="crosslink_bed_stats" file="chrM:4000-8300.crosslink_sites.test4.bed.stats"/>
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293 </test>
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294 </tests>
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295 <help><![CDATA[
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296
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297 PureCLIP is a tool to detect protein-RNA interaction footprints from single-nucleotide CLIP-seq data, such as iCLIP and eCLIP. It accepts mapped eCLIP/iCLIP reads in BAM format as input and also supports control library and crosslink-associated (CL) motifs input for bias correction.
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298
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299 PureCLIP outputs two BED files, containing the found crosslink sites (first file) and binding regions (second file) that merge nearby crosslink sites to contiguous regions (region width controlled by -dm parameter).
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300
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301 By default, the tool parameters are set to values optimized for proteins binding to short defined binding regions, e.g. proteins binding to short specific motifs such as PUM2 and RBFOX2. This behaviour can be changed with the -bc option. The default setting -bc 0 is equivalent to manually setting -bdwn 50 -ntp 10 -ntp2 0 -b1p 0.01 -b2p 0.15. The second setting -bc 1 is designed for RBPs that produce larger clusters (proteins causing larger crosslink clusters with relatively lower read start counts, e.g. proteins binding to low complexity motifs). -bc 1 corresponds to the manual setting -bdwn 100 -antp -b2p 0.01 -b2p 0.1.
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302
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303 In case of different binding characteristics, you can manually adjust parameters -bdw, -bdwn, -b1p, -b2p, -antp or have a look at the online documentation for more details:
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304
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305 http://pureclip.readthedocs.io/en/latest/index.html
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306
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307 ]]></help>
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308 <citations>
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309 <citation type="doi">10.1186/s13059-017-1364-2</citation>
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310 </citations>
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311 </tool>