Mercurial > repos > mvdbeek > damidseq_core

comparison damidseq_core.xml @ 8:621837e9bfed draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 5bf4f4dbd82988d1612d951d69125bc5f5b439be
author mvdbeek
date Thu, 03 May 2018 05:12:02 -0400
parents 02f09108bcff
children
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7:02f09108bcff 8:621837e9bfed
1 <tool id="damidseq_core" name="damidseq" version="0.1.4"> 1 <tool id="damidseq_core" name="damidseq" version="0.1.5">
2 <description>align, extend and normalize a DamID-seq experiment</description> 2 <description>align, extend and normalize a DamID-seq experiment</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.4">damidseq_pipeline</requirement> 4 <requirement type="package" version="1.4">damidseq_pipeline</requirement>
5 </requirements> 5 </requirements>
6 <version_command><![CDATA[damidseq_pipeline --help 2>&1| grep damidseq_pipeline]]></version_command> 6 <version_command><![CDATA[damidseq_pipeline --help 2>&1| grep damidseq_pipeline]]></version_command>
28 --q=$q 28 --q=$q
29 --qscore1max=$qscore1max 29 --qscore1max=$qscore1max
30 --qscore1min=$qscore1min 30 --qscore1min=$qscore1min
31 --qscore2max=$qscore2max 31 --qscore2max=$qscore2max
32 --threads=\${GALAXY_SLOTS:-4} 2>&1| LC_ALL=C sed -e 's/[^A-Za-z0-9._-]/ /g' && 32 --threads=\${GALAXY_SLOTS:-4} 2>&1| LC_ALL=C sed -e 's/[^A-Za-z0-9._-]/ /g' &&
33 mv Fusion-vs-Dam.gatc.* gatc.output 33 #set EXT = "-ext%s" % $len if $extend_reads == '1' else ""
34 mv 'Dam-${dam.element_identifier}${EXT}.bam' '$control_output' &&
35 mv '${dam_fusion.element_identifier}${EXT}.bam' '$fusion_output' &&
36 mv '${dam_fusion.element_identifier}-vs-Dam.gatc.$output_format' gatc.output
34 #if str($full_data_files): 37 #if str($full_data_files):
35 && mv Fusion-vs-Dam.* full.output 38 && mv '${dam_fusion.element_identifier}-vs-Dam.$output_format' full.output
36 #end if 39 #end if
37 ]]></command> 40 ]]></command>
38 <configfiles> 41 <configfiles>
39 <configfile name="index">A1 Dam 42 <configfile name="index">A1 Dam-$dam.element_identifier
40 A2 Fusion</configfile> 43 A2 $dam_fusion.element_identifier</configfile>
41 </configfiles> 44 </configfiles>
42 <inputs> 45 <inputs>
43 <param name="dam_fusion" type="data" format="fastq,fastq.gz" label="Dam fusion fastq"/> 46 <param name="dam_fusion" type="data" format="fastq,fastq.gz" label="Dam fusion fastq"/>
44 <param argument="--dam" type="data" format="fastq,fastq.gz" label="Control Dam fastq"/> 47 <param argument="--dam" type="data" format="fastq,fastq.gz" label="Control Dam fastq"/>
45 <param name="reference_index" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> 48 <param name="reference_index" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
73 <param argument="--qscore1min" type="float" min="0.0" value="0.4" max="1.0" label="min decile for normalising from Dam array"/> 76 <param argument="--qscore1min" type="float" min="0.0" value="0.4" max="1.0" label="min decile for normalising from Dam array"/>
74 <param argument="--qscore1max" type="float" min="0.0" value="1.0" max="1.0" label="max decile for normalising from Dam array"/> 77 <param argument="--qscore1max" type="float" min="0.0" value="1.0" max="1.0" label="max decile for normalising from Dam array"/>
75 <param argument="--qscore2max" type="float" min="0.0" value="0.9" max="1.0" label="max decile for normalising from fusion-protein array"/> 78 <param argument="--qscore2max" type="float" min="0.0" value="0.9" max="1.0" label="max decile for normalising from fusion-protein array"/>
76 </inputs> 79 </inputs>
77 <outputs> 80 <outputs>
78 <data name="output_ratio" format="bedgraph" from_work_dir="gatc.output" label="Dam-fusion vs Dam-only GATC ratio on ${on_string}"> 81 <data name="output_ratio" format="bedgraph" from_work_dir="gatc.output" label="Dam-fusion vs Dam-only GATC ratio on ${on_string}" default_identifier_source="dam_fusion">
79 <change_format> 82 <change_format>
80 <when input="output_format" value="gff" format="gff" /> 83 <when input="output_format" value="gff" format="gff" />
81 </change_format> 84 </change_format>
82 <actions> 85 <actions>
83 <action type="metadata" name="dbkey"> 86 <action type="metadata" name="dbkey">
86 <filter type="param_value" ref="reference_index" column="0"/> 89 <filter type="param_value" ref="reference_index" column="0"/>
87 </option> 90 </option>
88 </action> 91 </action>
89 </actions> 92 </actions>
90 </data> 93 </data>
91 <data name="output_ratio_full" format="bedgraph" from_work_dir="full.output" label="Dam-fusion vs Dam-only full ratio on ${on_string}"> 94 <data name="output_ratio_full" format="bedgraph" from_work_dir="full.output" label="Dam-fusion vs Dam-only full ratio on ${on_string}" default_identifier_source="dam_fusion">
92 <filter>full_data_files</filter> 95 <filter>full_data_files</filter>
93 <change_format> 96 <change_format>
94 <when input="output_format" value="gff" format="gff" /> 97 <when input="output_format" value="gff" format="gff" />
95 </change_format> 98 </change_format>
96 <actions> 99 <actions>
100 <filter type="param_value" ref="reference_index" column="0"/> 103 <filter type="param_value" ref="reference_index" column="0"/>
101 </option> 104 </option>
102 </action> 105 </action>
103 </actions> 106 </actions>
104 </data> 107 </data>
105 <data name="control_output" format="bam" from_work_dir="Dam-ext300.bam" label="Dam-only alignment on ${on_string}"> 108 <data name="control_output" format="bam" label="Dam-only alignment on ${on_string}" default_identifier_source="dam_fusion">
106 <actions> 109 <actions>
107 <action type="metadata" name="dbkey"> 110 <action type="metadata" name="dbkey">
108 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0"> 111 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
109 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> 112 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
110 <filter type="param_value" ref="reference_index" column="0"/> 113 <filter type="param_value" ref="reference_index" column="0"/>
111 </option> 114 </option>
112 </action> 115 </action>
113 </actions> 116 </actions>
114 </data> 117 </data>
115 <data name="fusion_output" format="bam" from_work_dir="Fusion-ext300.bam" label="Dam-fusion alignment on ${on_string}"> 118 <data name="fusion_output" format="bam" label="Dam-fusion alignment on ${on_string}" default_identifier_source="dam_fusion">
116 <actions> 119 <actions>
117 <action type="metadata" name="dbkey"> 120 <action type="metadata" name="dbkey">
118 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0"> 121 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
119 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> 122 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
120 <filter type="param_value" ref="reference_index" column="0"/> 123 <filter type="param_value" ref="reference_index" column="0"/>
133 <output name="output_ratio" file="output_ratio.bed"/> 136 <output name="output_ratio" file="output_ratio.bed"/>
134 <output name="control_output" file="control.bam"/> 137 <output name="control_output" file="control.bam"/>
135 <output name="fusion_output" file="fusion.bam"/> 138 <output name="fusion_output" file="fusion.bam"/>
136 </test> 139 </test>
137 <test> 140 <test>
141 <!-- test full data output -->
138 <param name="dam" value="A001.fastq"/> 142 <param name="dam" value="A001.fastq"/>
139 <param name="dam_fusion" value="A002.fastq"/> 143 <param name="dam_fusion" value="A002.fastq"/>
140 <param name="gatc_frag_file" value="dm6.GATC.gff"/> 144 <param name="gatc_frag_file" value="dm6.GATC.gff"/>
141 <param name="reference_index" value="dm6"/> 145 <param name="reference_index" value="dm6"/>
142 <param name="norm_method" value="rpm"/> 146 <param name="norm_method" value="rpm"/>
143 <param name="full_data_files" value="true"/> 147 <param name="full_data_files" value="true"/>
144 <output name="output_ratio" file="output_ratio.bed"/> 148 <output name="output_ratio" file="output_ratio.bed"/>
145 <output name="output_ratio_full" file="output_ratio_full.bed"/> 149 <output name="output_ratio_full" file="output_ratio_full.bed"/>
146 <output name="control_output" file="control.bam"/> 150 <output name="control_output" file="control.bam"/>
147 <output name="fusion_output" file="fusion.bam"/> 151 <output name="fusion_output" file="fusion.bam"/>
152 </test>
153 <test>
154 <!-- test no extension and gff outpt -->
155 <param name="dam" value="A001.fastq"/>
156 <param name="dam_fusion" value="A002.fastq"/>
157 <param name="gatc_frag_file" value="dm6.GATC.gff"/>
158 <param name="reference_index" value="dm6"/>
159 <param name="norm_method" value="rpm"/>
160 <param name="full_data_files" value="true"/>
161 <param name="extend_reads" value="false"/>
162 <param name="output_format" value="gff"/>
163 <output name="output_ratio" file="output_ratio2.gff"/>
164 <output name="output_ratio_full" file="output_ratio_full2.gff"/>
165 <output name="control_output" file="control2.bam"/>
166 <output name="fusion_output" file="fusion2.bam"/>
148 </test> 167 </test>
149 </tests> 168 </tests>
150 <help><![CDATA[ 169 <help><![CDATA[
151 170
152 Processing DamID-seq data involves extending single-end reads, aligning 171 Processing DamID-seq data involves extending single-end reads, aligning